Last week we learned about tools to deal with biological sequences with BioPython
.
Sequence analysis is very important, but ultimately, biological function is determined by structure.
Here is the (partial) sequence for a dopamine transporter protein:
DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVP
LFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNR
SEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIY
KAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEG
PGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQ
GGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPL
TYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQ
This protein's job is to take the dopamine neurotransmitter out of the neuron's synapses and terminate that feel-good positive response we get from dopamine.
This big string of text doesn't tell us much about how it can actually do this.
Structural biologists are able to determine what that sequence looks like when it takes its natural shape in the cell.
Here is that sequence's structure in 3D.
Clearly there is a lot more information coded in the sequence that we need to consider.
Today I'll walk you through extracting some useful information from this particular protein using BioPython's PDB
module.
Biomolecules such as proteins, RNA, DNA, and chemicals (such as dopamine) are made up of atoms.
Each atom occupies a point in 4 dimensions: X, Y, Z, and time. For now we will forget about time and only deal with fixed shapshots of atoms.
Structural biologists isolate molecules in the lab, and using tools such as X-ray crystallography can obtain the X, Y, and Z coordinates of all the atoms in the molecule.
This is the famous X-ray diffraction pattern of DNA used by Watson & Crick & Franklin to solve the double helix structure of DNA.
Other notable structure solving technologies: electron microscopy, cryo-electron microscopy, Nuclear Magnetic Resonance (NMR).
We don't have to worry about how they did it, but for many years now, solved structures (3D positions of biomolecules atoms) have been deposited in the RCSB PDB Database
Every entry in the database has a unique ID code.
The dopamine transporter we are interested in is: 4XP1
The main file format for sequences is FASTA
, for structures it is PDB
or mmCIF
.
BioPython.PDB has parsers for both.
Here is the main BioPython.PDB reference page.
We can automatically download a structure from the database using the PDBList
object's method retrieve_pdb_file
.
from Bio.PDB import *
pdbl = PDBList()
pdbl.retrieve_pdb_file('4XP1')
Structure exists: '/Users/carlosgonzalezoliver/Projects/Notebooks/COMP_364/L27/xp/4xp1.cif'
WARNING: The default download format has changed from PDB to PDBx/mmCif
'/Users/carlosgonzalezoliver/Projects/Notebooks/COMP_364/L27/xp/4xp1.cif'
That warning tells us that the PDB format is deprecated and that the new default is mmCIF.
We'll go into what that looks like in a little bit.
Now we should have a folder containing 4XP1.cif
in our working directory.
import os
os.listdir()
['.ipynb_checkpoints', '4xp1.cif', 'L27.ipynb', 'obsolete', 'xp']
os.listdir('xp')
['4xp1.cif']
parser = MMCIFParser()
The first argument to the instance method get_structure
is an optional name for the molecule, and the second argument is the path to the structure file.
structure = parser.get_structure('4XP1', 'xp/4xp1.cif')
/Users/carlosgonzalezoliver/anaconda/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:84: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 7477. PDBConstructionWarning) /Users/carlosgonzalezoliver/anaconda/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:84: PDBConstructionWarning: WARNING: Chain L is discontinuous at line 7658. PDBConstructionWarning) /Users/carlosgonzalezoliver/anaconda/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:84: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 7659. PDBConstructionWarning) /Users/carlosgonzalezoliver/anaconda/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:84: PDBConstructionWarning: WARNING: Chain L is discontinuous at line 7674. PDBConstructionWarning) /Users/carlosgonzalezoliver/anaconda/envs/py36/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:84: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 7677. PDBConstructionWarning)
Now we have extracted all the structural information from the file.
Let's take a peek at the attributes.
def cleandir(obj):
print(", ".join([a for a in dir(obj) if not a.startswith("_")]))
cleandir(structure)
add, child_dict, child_list, copy, detach_child, detach_parent, full_id, get_atoms, get_chains, get_full_id, get_id, get_iterator, get_level, get_list, get_models, get_parent, get_residues, has_id, header, id, insert, level, parent, set_parent, transform, xtra
Structure objects are organized in a specific hierarchy of objects.
We're just going to focus on the core elements which are: Model --> Chain --> Residue --> Atom.
Each structure file can contain multiple "models" of the same molecule.
Each model contains several "chains" or strands of protein/RNA/DNA/.
Each "chain" is made up of residues, or amino acids/DNA bases/RNA bases.
Each residue is made up of Atoms.
There is a very nice "widget" for notebooks that lets us visualize structure objects.
conda config --add channels conda-forge
conda install nglview -c bioconda
# might need: jupyter-nbextension enable nglview --py --sys-prefix
To do more advanced manipulations, it is better to use standalone tools such as Chimera and pyMOL.
Let's view our dopamine transporter protein bound to dopamine.
import nglview as nv
view = nv.show_biopython(structure)
view.clear_representations()
#view as ball and stick (atom and bond)
view.add_ball_and_stick()
view
A Jupyter Widget
As expected, we see a bunch of atoms in 3D space.
This can often be hard to look at so we usually visualize this with what's known as a "ribbon" representation.
view.clear_representations()
#add ribbons
view.add_cartoon('protein')
#add ball and stick for non-rotien
view.add_ball_and_stick('not protein')
view
A Jupyter Widget
Individual atoms are not shown and instead, each chain is visualized as a continuous ribbon.
We can see here that we have 3 different chains and a couple of ligands.
Let's see how we can get a handle on the different components.
How many models are there in this structure? It looks like there is only one transporter protein so we should only have a single model.
for model in structure:
print(f"model {model}")
model <Model id=0>
Ok we have one model.
But we should have several chains as we saw above.
model = structure[0] #since we only have one model
for chain in model:
print(f"chain {chain}, Chain ID: {chain.id}")
chain <Chain id=A>, Chain ID: A chain <Chain id=L>, Chain ID: L chain <Chain id=H>, Chain ID: H
Ok as we guessed, we have 3 chains: A, L, and H.
We can go one step further and get all the residues in a chain.
We can access individual chains like keys in a dictionary from a model.
chain_A = model['A']
for res in chain_A:
print(f"Residue name: {res.resname}, number: {res.id[1]}")
Residue name: ASP, number: 25 Residue name: GLU, number: 26 Residue name: ARG, number: 27 Residue name: GLU, number: 28 Residue name: THR, number: 29 Residue name: TRP, number: 30 Residue name: SER, number: 31 Residue name: GLY, number: 32 Residue name: LYS, number: 33 Residue name: VAL, number: 34 Residue name: ASP, number: 35 Residue name: PHE, number: 36 Residue name: LEU, number: 37 Residue name: LEU, number: 38 Residue name: SER, number: 39 Residue name: VAL, number: 40 Residue name: ILE, number: 41 Residue name: GLY, number: 42 Residue name: PHE, number: 43 Residue name: ALA, number: 44 Residue name: VAL, number: 45 Residue name: ASP, number: 46 Residue name: LEU, number: 47 Residue name: ALA, number: 48 Residue name: ASN, number: 49 Residue name: VAL, number: 50 Residue name: TRP, number: 51 Residue name: ARG, number: 52 Residue name: PHE, number: 53 Residue name: PRO, number: 54 Residue name: TYR, number: 55 Residue name: LEU, number: 56 Residue name: CYS, number: 57 Residue name: TYR, number: 58 Residue name: LYS, number: 59 Residue name: ASN, number: 60 Residue name: GLY, number: 61 Residue name: GLY, number: 62 Residue name: GLY, number: 63 Residue name: ALA, number: 64 Residue name: PHE, number: 65 Residue name: LEU, number: 66 Residue name: VAL, number: 67 Residue name: PRO, number: 68 Residue name: TYR, number: 69 Residue name: GLY, number: 70 Residue name: ILE, number: 71 Residue name: MET, number: 72 Residue name: LEU, number: 73 Residue name: ALA, number: 74 Residue name: VAL, number: 75 Residue name: GLY, number: 76 Residue name: GLY, number: 77 Residue name: ILE, number: 78 Residue name: PRO, number: 79 Residue name: LEU, number: 80 Residue name: PHE, number: 81 Residue name: TYR, number: 82 Residue name: MET, number: 83 Residue name: GLU, number: 84 Residue name: LEU, number: 85 Residue name: ALA, number: 86 Residue name: LEU, number: 87 Residue name: GLY, number: 88 Residue name: GLN, number: 89 Residue name: HIS, number: 90 Residue name: ASN, number: 91 Residue name: ARG, number: 92 Residue name: LYS, number: 93 Residue name: GLY, number: 94 Residue name: ALA, number: 95 Residue name: ILE, number: 96 Residue name: THR, number: 97 Residue name: CYS, number: 98 Residue name: TRP, number: 99 Residue name: GLY, number: 100 Residue name: ARG, number: 101 Residue name: LEU, number: 102 Residue name: VAL, number: 103 Residue name: PRO, number: 104 Residue name: LEU, number: 105 Residue name: PHE, number: 106 Residue name: LYS, number: 107 Residue name: GLY, number: 108 Residue name: ILE, number: 109 Residue name: GLY, number: 110 Residue name: TYR, number: 111 Residue name: ALA, number: 112 Residue name: VAL, number: 113 Residue name: VAL, number: 114 Residue name: LEU, number: 115 Residue name: ILE, number: 116 Residue name: ALA, number: 117 Residue name: PHE, number: 118 Residue name: TYR, number: 119 Residue name: VAL, number: 120 Residue name: ASP, number: 121 Residue name: PHE, number: 122 Residue name: TYR, number: 123 Residue name: TYR, number: 124 Residue name: ASN, number: 125 Residue name: VAL, number: 126 Residue name: ILE, number: 127 Residue name: ILE, number: 128 Residue name: ALA, number: 129 Residue name: TRP, number: 130 Residue name: SER, number: 131 Residue name: LEU, number: 132 Residue name: ARG, number: 133 Residue name: PHE, number: 134 Residue name: PHE, number: 135 Residue name: PHE, number: 136 Residue name: ALA, number: 137 Residue name: SER, number: 138 Residue name: PHE, number: 139 Residue name: THR, number: 140 Residue name: ASN, number: 141 Residue name: SER, number: 142 Residue name: LEU, number: 143 Residue name: PRO, number: 144 Residue name: TRP, number: 145 Residue name: THR, number: 146 Residue name: SER, number: 147 Residue name: CYS, number: 148 Residue name: ASN, number: 149 Residue name: ASN, number: 150 Residue name: ILE, number: 151 Residue name: TRP, number: 152 Residue name: ASN, number: 153 Residue name: THR, number: 154 Residue name: PRO, number: 155 Residue name: ASN, number: 156 Residue name: CYS, number: 157 Residue name: ARG, number: 158 Residue name: PRO, number: 159 Residue name: PHE, number: 160 Residue name: GLU, number: 161 Residue name: GLY, number: 203 Residue name: HIS, number: 204 Residue name: VAL, number: 205 Residue name: GLU, number: 206 Residue name: GLY, number: 207 Residue name: PHE, number: 208 Residue name: GLN, number: 209 Residue name: SER, number: 210 Residue name: ALA, number: 211 Residue name: ALA, number: 212 Residue name: SER, number: 213 Residue name: GLU, number: 214 Residue name: TYR, number: 215 Residue name: PHE, number: 216 Residue name: ASN, number: 217 Residue name: ARG, number: 218 Residue name: TYR, number: 219 Residue name: ILE, number: 220 Residue name: LEU, number: 221 Residue name: GLU, number: 222 Residue name: LEU, number: 223 Residue name: ASN, number: 224 Residue name: ARG, number: 225 Residue name: SER, number: 226 Residue name: GLU, number: 227 Residue name: GLY, number: 228 Residue name: ILE, number: 229 Residue name: HIS, number: 230 Residue name: ASP, number: 231 Residue name: LEU, number: 232 Residue name: GLY, number: 233 Residue name: ALA, number: 234 Residue name: ILE, number: 235 Residue name: LYS, number: 236 Residue name: TRP, number: 237 Residue name: ASP, number: 238 Residue name: MET, number: 239 Residue name: ALA, number: 240 Residue name: LEU, number: 241 Residue name: CYS, number: 242 Residue name: LEU, number: 243 Residue name: LEU, number: 244 Residue name: ILE, number: 245 Residue name: VAL, number: 246 Residue name: TYR, number: 247 Residue name: LEU, number: 248 Residue name: ILE, number: 249 Residue name: CYS, number: 250 Residue name: TYR, number: 251 Residue name: PHE, number: 252 Residue name: SER, number: 253 Residue name: LEU, number: 254 Residue name: TRP, number: 255 Residue name: LYS, number: 256 Residue name: GLY, number: 257 Residue name: ILE, number: 258 Residue name: SER, number: 259 Residue name: THR, number: 260 Residue name: SER, number: 261 Residue name: GLY, number: 262 Residue name: LYS, number: 263 Residue name: VAL, number: 264 Residue name: VAL, number: 265 Residue name: TRP, number: 266 Residue name: PHE, number: 267 Residue name: THR, number: 268 Residue name: ALA, number: 269 Residue name: LEU, number: 270 Residue name: PHE, number: 271 Residue name: PRO, number: 272 Residue name: TYR, number: 273 Residue name: ALA, number: 274 Residue name: VAL, number: 275 Residue name: LEU, number: 276 Residue name: LEU, number: 277 Residue name: ILE, number: 278 Residue name: LEU, number: 279 Residue name: LEU, number: 280 Residue name: ILE, number: 281 Residue name: ARG, number: 282 Residue name: GLY, number: 283 Residue name: LEU, number: 284 Residue name: THR, number: 285 Residue name: LEU, number: 286 Residue name: PRO, number: 287 Residue name: GLY, number: 288 Residue name: SER, number: 289 Residue name: PHE, number: 290 Residue name: LEU, number: 291 Residue name: GLY, number: 292 Residue name: ILE, number: 293 Residue name: GLN, number: 294 Residue name: TYR, number: 295 Residue name: TYR, number: 296 Residue name: LEU, number: 297 Residue name: THR, number: 298 Residue name: PRO, number: 299 Residue name: ASN, number: 300 Residue name: PHE, number: 301 Residue name: SER, number: 302 Residue name: ALA, number: 303 Residue name: ILE, number: 304 Residue name: TYR, number: 305 Residue name: LYS, number: 306 Residue name: ALA, number: 307 Residue name: GLU, number: 308 Residue name: VAL, number: 309 Residue name: TRP, number: 310 Residue name: VAL, number: 311 Residue name: ASP, number: 312 Residue name: ALA, number: 313 Residue name: ALA, number: 314 Residue name: THR, number: 315 Residue name: GLN, number: 316 Residue name: VAL, number: 317 Residue name: PHE, number: 318 Residue name: PHE, number: 319 Residue name: SER, number: 320 Residue name: LEU, number: 321 Residue name: GLY, number: 322 Residue name: PRO, number: 323 Residue name: GLY, number: 324 Residue name: PHE, number: 325 Residue name: GLY, number: 326 Residue name: VAL, number: 327 Residue name: LEU, number: 328 Residue name: LEU, number: 329 Residue name: ALA, number: 330 Residue name: TYR, number: 331 Residue name: ALA, number: 332 Residue name: SER, number: 333 Residue name: TYR, number: 334 Residue name: ASN, number: 335 Residue name: LYS, number: 336 Residue name: TYR, number: 337 Residue name: HIS, number: 338 Residue name: ASN, number: 339 Residue name: ASN, number: 340 Residue name: VAL, number: 341 Residue name: TYR, number: 342 Residue name: LYS, number: 343 Residue name: ASP, number: 344 Residue name: ALA, number: 345 Residue name: LEU, number: 346 Residue name: LEU, number: 347 Residue name: THR, number: 348 Residue name: SER, number: 349 Residue name: PHE, number: 350 Residue name: ILE, number: 351 Residue name: ASN, number: 352 Residue name: SER, number: 353 Residue name: ALA, number: 354 Residue name: THR, number: 355 Residue name: SER, number: 356 Residue name: PHE, number: 357 Residue name: ILE, number: 358 Residue name: ALA, number: 359 Residue name: GLY, number: 360 Residue name: PHE, number: 361 Residue name: VAL, number: 362 Residue name: ILE, number: 363 Residue name: PHE, number: 364 Residue name: SER, number: 365 Residue name: VAL, number: 366 Residue name: LEU, number: 367 Residue name: GLY, number: 368 Residue name: TYR, number: 369 Residue name: MET, number: 370 Residue name: ALA, number: 371 Residue name: HIS, number: 372 Residue name: THR, number: 373 Residue name: LEU, number: 374 Residue name: GLY, number: 375 Residue name: VAL, number: 376 Residue name: ARG, number: 377 Residue name: ILE, number: 378 Residue name: GLU, number: 379 Residue name: ASP, number: 380 Residue name: VAL, number: 381 Residue name: ALA, number: 382 Residue name: THR, number: 383 Residue name: GLU, number: 384 Residue name: GLY, number: 385 Residue name: PRO, number: 386 Residue name: GLY, number: 387 Residue name: LEU, number: 388 Residue name: VAL, number: 389 Residue name: PHE, number: 390 Residue name: VAL, number: 391 Residue name: VAL, number: 392 Residue name: TYR, number: 393 Residue name: PRO, number: 394 Residue name: ALA, number: 395 Residue name: ALA, number: 396 Residue name: ILE, number: 397 Residue name: ALA, number: 398 Residue name: THR, number: 399 Residue name: MET, number: 400 Residue name: PRO, number: 401 Residue name: ALA, number: 402 Residue name: SER, number: 403 Residue name: THR, number: 404 Residue name: PHE, number: 405 Residue name: TRP, number: 406 Residue name: ALA, number: 407 Residue name: LEU, number: 408 Residue name: ILE, number: 409 Residue name: PHE, number: 410 Residue name: PHE, number: 411 Residue name: MET, number: 412 Residue name: MET, number: 413 Residue name: LEU, number: 414 Residue name: ALA, number: 415 Residue name: THR, number: 416 Residue name: LEU, number: 417 Residue name: GLY, number: 418 Residue name: LEU, number: 419 Residue name: ASP, number: 420 Residue name: SER, number: 421 Residue name: SER, number: 422 Residue name: PHE, number: 423 Residue name: GLY, number: 424 Residue name: GLY, number: 425 Residue name: SER, number: 426 Residue name: GLU, number: 427 Residue name: ALA, number: 428 Residue name: ILE, number: 429 Residue name: ILE, number: 430 Residue name: THR, number: 431 Residue name: ALA, number: 432 Residue name: LEU, number: 433 Residue name: SER, number: 434 Residue name: ASP, number: 435 Residue name: GLU, number: 436 Residue name: PHE, number: 437 Residue name: PRO, number: 438 Residue name: LYS, number: 439 Residue name: ILE, number: 440 Residue name: LYS, number: 441 Residue name: ARG, number: 442 Residue name: ASN, number: 443 Residue name: ARG, number: 444 Residue name: GLU, number: 445 Residue name: LEU, number: 446 Residue name: PHE, number: 447 Residue name: VAL, number: 448 Residue name: ALA, number: 449 Residue name: GLY, number: 450 Residue name: LEU, number: 451 Residue name: PHE, number: 452 Residue name: SER, number: 453 Residue name: LEU, number: 454 Residue name: TYR, number: 455 Residue name: PHE, number: 456 Residue name: VAL, number: 457 Residue name: VAL, number: 458 Residue name: GLY, number: 459 Residue name: LEU, number: 460 Residue name: ALA, number: 461 Residue name: SER, number: 462 Residue name: CYS, number: 463 Residue name: THR, number: 464 Residue name: GLN, number: 465 Residue name: GLY, number: 466 Residue name: GLY, number: 467 Residue name: PHE, number: 468 Residue name: TYR, number: 469 Residue name: PHE, number: 470 Residue name: PHE, number: 471 Residue name: HIS, number: 472 Residue name: LEU, number: 473 Residue name: LEU, number: 474 Residue name: ASP, number: 475 Residue name: ARG, number: 476 Residue name: TYR, number: 477 Residue name: ALA, number: 478 Residue name: ALA, number: 479 Residue name: GLY, number: 480 Residue name: TYR, number: 481 Residue name: SER, number: 482 Residue name: ILE, number: 483 Residue name: LEU, number: 484 Residue name: VAL, number: 485 Residue name: ALA, number: 486 Residue name: VAL, number: 487 Residue name: PHE, number: 488 Residue name: PHE, number: 489 Residue name: GLU, number: 490 Residue name: ALA, number: 491 Residue name: ILE, number: 492 Residue name: ALA, number: 493 Residue name: VAL, number: 494 Residue name: SER, number: 495 Residue name: TRP, number: 496 Residue name: ILE, number: 497 Residue name: TYR, number: 498 Residue name: GLY, number: 499 Residue name: THR, number: 500 Residue name: ASN, number: 501 Residue name: ARG, number: 502 Residue name: PHE, number: 503 Residue name: SER, number: 504 Residue name: GLU, number: 505 Residue name: ASP, number: 506 Residue name: ILE, number: 507 Residue name: ARG, number: 508 Residue name: ASP, number: 509 Residue name: MET, number: 510 Residue name: ILE, number: 511 Residue name: GLY, number: 512 Residue name: PHE, number: 513 Residue name: PRO, number: 514 Residue name: PRO, number: 515 Residue name: GLY, number: 516 Residue name: ARG, number: 517 Residue name: TYR, number: 518 Residue name: TRP, number: 519 Residue name: GLN, number: 520 Residue name: VAL, number: 521 Residue name: CYS, number: 522 Residue name: TRP, number: 523 Residue name: ARG, number: 524 Residue name: PHE, number: 525 Residue name: VAL, number: 526 Residue name: ALA, number: 527 Residue name: PRO, number: 528 Residue name: ILE, number: 529 Residue name: PHE, number: 530 Residue name: LEU, number: 531 Residue name: LEU, number: 532 Residue name: PHE, number: 533 Residue name: ILE, number: 534 Residue name: THR, number: 535 Residue name: VAL, number: 536 Residue name: TYR, number: 537 Residue name: GLY, number: 538 Residue name: LEU, number: 539 Residue name: ILE, number: 540 Residue name: GLY, number: 541 Residue name: TYR, number: 542 Residue name: GLU, number: 543 Residue name: PRO, number: 544 Residue name: LEU, number: 545 Residue name: THR, number: 546 Residue name: TYR, number: 547 Residue name: ALA, number: 548 Residue name: ASP, number: 549 Residue name: TYR, number: 550 Residue name: VAL, number: 551 Residue name: TYR, number: 552 Residue name: PRO, number: 553 Residue name: SER, number: 554 Residue name: TRP, number: 555 Residue name: ALA, number: 556 Residue name: ASN, number: 557 Residue name: ALA, number: 558 Residue name: LEU, number: 559 Residue name: GLY, number: 560 Residue name: TRP, number: 561 Residue name: CYS, number: 562 Residue name: ILE, number: 563 Residue name: ALA, number: 564 Residue name: GLY, number: 565 Residue name: SER, number: 566 Residue name: SER, number: 567 Residue name: VAL, number: 568 Residue name: VAL, number: 569 Residue name: MET, number: 570 Residue name: ILE, number: 571 Residue name: PRO, number: 572 Residue name: ALA, number: 573 Residue name: VAL, number: 574 Residue name: ALA, number: 575 Residue name: ILE, number: 576 Residue name: PHE, number: 577 Residue name: LYS, number: 578 Residue name: LEU, number: 579 Residue name: LEU, number: 580 Residue name: SER, number: 581 Residue name: THR, number: 582 Residue name: PRO, number: 583 Residue name: GLY, number: 584 Residue name: SER, number: 585 Residue name: LEU, number: 586 Residue name: ARG, number: 587 Residue name: GLN, number: 588 Residue name: ARG, number: 589 Residue name: PHE, number: 590 Residue name: THR, number: 591 Residue name: ILE, number: 592 Residue name: LEU, number: 593 Residue name: THR, number: 594 Residue name: THR, number: 595 Residue name: PRO, number: 596 Residue name: TRP, number: 597 Residue name: ARG, number: 598 Residue name: ASP, number: 599 Residue name: GLN, number: 600 Residue name: NA, number: 701 Residue name: NA, number: 702 Residue name: CL, number: 703 Residue name: MAL, number: 704 Residue name: MAL, number: 705 Residue name: NAG, number: 706 Residue name: P4G, number: 707 Residue name: LDP, number: 708 Residue name: EDO, number: 709 Residue name: Y01, number: 710 Residue name: CLR, number: 711 Residue name: HOH, number: 801 Residue name: HOH, number: 802 Residue name: HOH, number: 803 Residue name: HOH, number: 804 Residue name: HOH, number: 805 Residue name: HOH, number: 806 Residue name: HOH, number: 807 Residue name: HOH, number: 808 Residue name: HOH, number: 809 Residue name: HOH, number: 810 Residue name: HOH, number: 811 Residue name: HOH, number: 812 Residue name: HOH, number: 813 Residue name: HOH, number: 814 Residue name: HOH, number: 815
Now we see that each chain is made up of Residue
objects.
Finally, each residue should be made up of atoms.
Let's get residue 56 from Chain A.
res = chain_A[56]
print(res)
<Residue LEU het= resseq=56 icode= >
for atom in res:
print(f"{atom.name}")
N CA C O CB CG CD1 CD2
Putting it all together, we can print every atom in every chain.
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
print(atom)
<Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Disordered Atom CA> <Atom C> <Atom O> <Disordered Atom CB> <Disordered Atom CG> <Disordered Atom SD> <Disordered Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> 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CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> 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<Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> 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NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> 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<Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom NA> <Atom NA> <Atom CL> <Atom C1> <Atom C2> <Atom C3> <Atom C4> <Atom C5> <Atom C6> <Atom O1> <Atom O2> <Atom O3> <Atom O4> <Atom O5> <Atom O6> <Atom C1'> <Atom C2'> <Atom C3'> <Atom C4'> <Atom C5'> <Atom C6'> <Atom O1'> <Atom O2'> <Atom O3'> <Atom O5'> <Atom O6'> <Atom C1> <Atom C2> <Atom C3> <Atom C4> <Atom C5> <Atom C6> <Atom O1> <Atom O2> <Atom O3> <Atom O4> <Atom O5> <Atom O6> <Atom C1'> <Atom C2'> <Atom C3'> <Atom C4'> <Atom C5'> <Atom C6'> <Atom O1'> <Atom O2'> <Atom O3'> <Atom O5'> <Atom O6'> <Atom C1> <Atom C2> <Atom C3> <Atom C4> <Atom C5> <Atom C6> <Atom C7> <Atom C8> <Atom N2> <Atom O3> <Atom O4> <Atom O5> <Atom O6> <Atom O7> <Atom C8> <Atom C7> <Atom O4> <Atom C6> <Atom C5> <Atom O3> <Atom C4> <Atom C3> <Atom O2> <Atom C2> <Atom C1> <Atom H81> <Atom H82> <Atom H83> <Atom H71> <Atom H72> <Atom H61> <Atom H62> <Atom H51> <Atom H52> <Atom H41> <Atom H42> <Atom H31> <Atom H32> <Atom H21> <Atom H22> <Atom H11> <Atom H12> <Atom H13> <Atom C7> <Atom C1> <Atom C4> <Atom C2> <Atom C6> <Atom C5> <Atom C3> <Atom O1> <Atom O2> <Atom C8> <Atom N1> <Atom H71> <Atom H72> <Atom H2> <Atom H6> <Atom H5> <Atom HO1> <Atom HO2> <Atom H81> <Atom H82> <Atom HN11> <Atom HN12> <Atom C1> <Atom O1> <Atom C2> <Atom O2> <Atom CAA> <Atom CBA> <Atom CAB> <Atom CAN> <Atom CAJ> <Atom CAO> <Atom CBB> <Atom CAC> <Atom CBE> <Atom CAP> <Atom CAQ> <Atom CBG> <Atom CBI> <Atom CAE> <Atom CAU> <Atom CAS> <Atom CBF> <Atom CBD> <Atom CAK> <Atom CAI> <Atom CAZ> <Atom CAV> <Atom CBH> <Atom CAD> <Atom CAT> <Atom CAR> <Atom CBC> <Atom OAW> <Atom CAY> <Atom OAG> <Atom CAM> <Atom CAL> <Atom CAX> <Atom OAH> <Atom OAF> <Atom C1> <Atom C2> <Atom C3> <Atom C4> <Atom C5> <Atom C6> <Atom C7> <Atom C8> <Atom C9> <Atom C10> <Atom C11> <Atom C12> <Atom C13> <Atom C14> <Atom C15> <Atom C16> <Atom C17> <Atom C18> <Atom C19> <Atom C20> <Atom C21> <Atom C22> <Atom C23> <Atom C24> <Atom C25> <Atom C26> <Atom C27> <Atom O1> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom NA> <Atom O> <Atom O> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom SD> <Atom CE> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom NE> <Atom CZ> <Atom NH1> <Atom NH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom CE1> <Atom CE2> <Atom CZ> <Atom OH> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD1> <Atom CD2> <Atom NE1> <Atom CE2> <Atom CE3> <Atom CZ2> <Atom CZ3> <Atom CH2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom SG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom ND2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom ND1> <Atom CD2> <Atom CE1> <Atom NE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom OG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom OD1> <Atom OD2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom CE> <Atom NZ> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG1> <Atom CG2> <Atom CD1> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom OE1> <Atom OE2> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom CG> <Atom CD> <Atom N> <Atom CA> <Atom C> <Atom O> <Atom CB> <Atom O> <Atom O> <Atom O>
Let's say I want to design a drug that binds to the transporter and blocks it from binding to dopamine.
This should have the effect of making people happier because dopamine now won't be removed from the synapses.
Actually, that's exactly what many antidepressants and narcotics (cocaine, amphetamines) do.
In order to do this, we need to know which residues dopamine binds so we can design a chemical that targets these kinds of residues.
mmCIF files are like dictionaries with key:value pairs.
When we parsed the file above, we really only got the structure info, but there is a lot more information that we can access by parsing a little differently.
MMCIF files have a ton of information and they look like this:
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
D 4 NA 1 701 701 NA NA A .
E 4 NA 1 702 702 NA NA A .
F 5 CL 1 703 704 CL CL A .
G 6 MAL 1 704 1 MAL MAL A .
H 6 MAL 1 705 2 MAL MAL A .
I 7 NAG 1 706 1 NAG NAG A .
J 8 P4G 1 707 1 P4G P4G A .
K 9 LDP 1 708 2 LDP LDP A .
This happens to be an entry for "non-polymer" entities aka ligands/chemicals.
There are 10 _pdbx_nonpoly_scheme..
headers. Each corresponds to a label for the columns in the entries below.
So _pdbx_nonpoly_scheme.mon_id
corresponds to the third column which is the id
of the ligand.
The loop_
means, when parsing, loop over all the rows for each column label to make a list.
For example: _pdbx_nonpoly_scheme.asym_id
after looping would map to: ['D', 'E', 'F', 'G', ...]
We're interested in LDP
which is dopamine, but we see that there are others.
BioPython lets us parse this information into a dictionary.
struc_dict = MMCIF2Dict.MMCIF2Dict('xp/4xp1.cif')
print(struc_dict.keys())
dict_keys(['data_', '_entry.id', '_audit_conform.dict_name', '_audit_conform.dict_version', '_audit_conform.dict_location', '_database_2.database_id', '_database_2.database_code', '_pdbx_database_related.db_name', '_pdbx_database_related.details', '_pdbx_database_related.db_id', '_pdbx_database_related.content_type', '_pdbx_database_status.status_code', '_pdbx_database_status.status_code_sf', '_pdbx_database_status.status_code_mr', '_pdbx_database_status.entry_id', '_pdbx_database_status.recvd_initial_deposition_date', '_pdbx_database_status.SG_entry', '_pdbx_database_status.deposit_site', '_pdbx_database_status.process_site', '_pdbx_database_status.status_code_cs', '_pdbx_database_status.methods_development_category', '_pdbx_database_status.pdb_format_compatible', '_audit_author.name', '_audit_author.pdbx_ordinal', '_citation.abstract', '_citation.abstract_id_CAS', '_citation.book_id_ISBN', '_citation.book_publisher', '_citation.book_publisher_city', '_citation.book_title', '_citation.coordinate_linkage', '_citation.country', '_citation.database_id_Medline', '_citation.details', '_citation.id', '_citation.journal_abbrev', '_citation.journal_id_ASTM', '_citation.journal_id_CSD', '_citation.journal_id_ISSN', '_citation.journal_full', '_citation.journal_issue', '_citation.journal_volume', '_citation.language', '_citation.page_first', '_citation.page_last', '_citation.title', '_citation.year', '_citation.database_id_CSD', '_citation.pdbx_database_id_DOI', '_citation.pdbx_database_id_PubMed', '_citation.unpublished_flag', '_citation_author.citation_id', '_citation_author.name', '_citation_author.ordinal', '_cell.length_a', '_cell.length_b', '_cell.length_c', '_cell.angle_alpha', '_cell.angle_beta', '_cell.angle_gamma', '_cell.entry_id', '_cell.Z_PDB', '_cell.pdbx_unique_axis', '_symmetry.space_group_name_H-M', '_symmetry.entry_id', '_symmetry.Int_Tables_number', '_symmetry.pdbx_full_space_group_name_H-M', '_symmetry.cell_setting', '_entity.id', '_entity.type', '_entity.src_method', '_entity.pdbx_description', '_entity.formula_weight', '_entity.pdbx_number_of_molecules', '_entity.pdbx_ec', '_entity.pdbx_mutation', '_entity.pdbx_fragment', '_entity.details', '_entity_poly.entity_id', '_entity_poly.type', '_entity_poly.nstd_linkage', '_entity_poly.nstd_monomer', '_entity_poly.pdbx_seq_one_letter_code', '_entity_poly.pdbx_seq_one_letter_code_can', '_entity_poly.pdbx_strand_id', '_entity_poly.pdbx_target_identifier', '_entity_poly_seq.entity_id', '_entity_poly_seq.num', '_entity_poly_seq.mon_id', '_entity_poly_seq.hetero', '_entity_src_gen.entity_id', '_entity_src_gen.pdbx_src_id', '_entity_src_gen.pdbx_alt_source_flag', '_entity_src_gen.pdbx_seq_type', '_entity_src_gen.pdbx_beg_seq_num', '_entity_src_gen.pdbx_end_seq_num', '_entity_src_gen.gene_src_common_name', '_entity_src_gen.gene_src_genus', '_entity_src_gen.pdbx_gene_src_gene', '_entity_src_gen.gene_src_species', '_entity_src_gen.gene_src_strain', '_entity_src_gen.gene_src_tissue', '_entity_src_gen.gene_src_tissue_fraction', '_entity_src_gen.gene_src_details', '_entity_src_gen.pdbx_gene_src_fragment', '_entity_src_gen.pdbx_gene_src_scientific_name', '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id', '_entity_src_gen.pdbx_gene_src_variant', '_entity_src_gen.pdbx_gene_src_cell_line', '_entity_src_gen.pdbx_gene_src_atcc', '_entity_src_gen.pdbx_gene_src_organ', '_entity_src_gen.pdbx_gene_src_organelle', '_entity_src_gen.pdbx_gene_src_cell', '_entity_src_gen.pdbx_gene_src_cellular_location', '_entity_src_gen.host_org_common_name', '_entity_src_gen.pdbx_host_org_scientific_name', '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id', '_entity_src_gen.host_org_genus', '_entity_src_gen.pdbx_host_org_gene', '_entity_src_gen.pdbx_host_org_organ', '_entity_src_gen.host_org_species', '_entity_src_gen.pdbx_host_org_tissue', '_entity_src_gen.pdbx_host_org_tissue_fraction', '_entity_src_gen.pdbx_host_org_strain', '_entity_src_gen.pdbx_host_org_variant', '_entity_src_gen.pdbx_host_org_cell_line', '_entity_src_gen.pdbx_host_org_atcc', '_entity_src_gen.pdbx_host_org_culture_collection', '_entity_src_gen.pdbx_host_org_cell', '_entity_src_gen.pdbx_host_org_organelle', '_entity_src_gen.pdbx_host_org_cellular_location', '_entity_src_gen.pdbx_host_org_vector_type', '_entity_src_gen.pdbx_host_org_vector', '_entity_src_gen.host_org_details', '_entity_src_gen.expression_system_id', '_entity_src_gen.plasmid_name', '_entity_src_gen.plasmid_details', '_entity_src_gen.pdbx_description', '_struct_ref.id', '_struct_ref.db_name', '_struct_ref.db_code', '_struct_ref.pdbx_db_accession', '_struct_ref.pdbx_db_isoform', '_struct_ref.entity_id', '_struct_ref.pdbx_seq_one_letter_code', '_struct_ref.pdbx_align_begin', '_struct_ref_seq.align_id', '_struct_ref_seq.ref_id', '_struct_ref_seq.pdbx_PDB_id_code', '_struct_ref_seq.pdbx_strand_id', '_struct_ref_seq.seq_align_beg', '_struct_ref_seq.pdbx_seq_align_beg_ins_code', '_struct_ref_seq.seq_align_end', '_struct_ref_seq.pdbx_seq_align_end_ins_code', '_struct_ref_seq.pdbx_db_accession', '_struct_ref_seq.db_align_beg', '_struct_ref_seq.pdbx_db_align_beg_ins_code', '_struct_ref_seq.db_align_end', '_struct_ref_seq.pdbx_db_align_end_ins_code', '_struct_ref_seq.pdbx_auth_seq_align_beg', '_struct_ref_seq.pdbx_auth_seq_align_end', '_struct_ref_seq_dif.align_id', '_struct_ref_seq_dif.pdbx_pdb_id_code', '_struct_ref_seq_dif.mon_id', '_struct_ref_seq_dif.pdbx_pdb_strand_id', '_struct_ref_seq_dif.seq_num', '_struct_ref_seq_dif.pdbx_pdb_ins_code', '_struct_ref_seq_dif.pdbx_seq_db_name', '_struct_ref_seq_dif.pdbx_seq_db_accession_code', '_struct_ref_seq_dif.db_mon_id', '_struct_ref_seq_dif.pdbx_seq_db_seq_num', '_struct_ref_seq_dif.details', '_struct_ref_seq_dif.pdbx_auth_seq_num', '_struct_ref_seq_dif.pdbx_ordinal', '_chem_comp.id', '_chem_comp.type', '_chem_comp.mon_nstd_flag', '_chem_comp.name', '_chem_comp.pdbx_synonyms', '_chem_comp.formula', '_chem_comp.formula_weight', '_exptl.absorpt_coefficient_mu', '_exptl.absorpt_correction_T_max', '_exptl.absorpt_correction_T_min', '_exptl.absorpt_correction_type', '_exptl.absorpt_process_details', '_exptl.entry_id', '_exptl.crystals_number', '_exptl.details', '_exptl.method', '_exptl.method_details', '_exptl_crystal.colour', '_exptl_crystal.density_diffrn', '_exptl_crystal.density_Matthews', '_exptl_crystal.density_method', '_exptl_crystal.density_percent_sol', '_exptl_crystal.description', '_exptl_crystal.F_000', '_exptl_crystal.id', '_exptl_crystal.preparation', '_exptl_crystal.size_max', '_exptl_crystal.size_mid', '_exptl_crystal.size_min', '_exptl_crystal.size_rad', '_exptl_crystal.colour_lustre', '_exptl_crystal.colour_modifier', '_exptl_crystal.colour_primary', '_exptl_crystal.density_meas', '_exptl_crystal.density_meas_esd', '_exptl_crystal.density_meas_gt', '_exptl_crystal.density_meas_lt', '_exptl_crystal.density_meas_temp', '_exptl_crystal.density_meas_temp_esd', '_exptl_crystal.density_meas_temp_gt', '_exptl_crystal.density_meas_temp_lt', '_exptl_crystal.pdbx_crystal_image_url', '_exptl_crystal.pdbx_crystal_image_format', '_exptl_crystal.pdbx_mosaicity', '_exptl_crystal.pdbx_mosaicity_esd', '_exptl_crystal_grow.apparatus', '_exptl_crystal_grow.atmosphere', '_exptl_crystal_grow.crystal_id', '_exptl_crystal_grow.details', '_exptl_crystal_grow.method', '_exptl_crystal_grow.method_ref', '_exptl_crystal_grow.pH', '_exptl_crystal_grow.pressure', '_exptl_crystal_grow.pressure_esd', '_exptl_crystal_grow.seeding', '_exptl_crystal_grow.seeding_ref', '_exptl_crystal_grow.temp', '_exptl_crystal_grow.temp_details', '_exptl_crystal_grow.temp_esd', '_exptl_crystal_grow.time', '_exptl_crystal_grow.pdbx_details', '_exptl_crystal_grow.pdbx_pH_range', '_diffrn.ambient_environment', '_diffrn.ambient_temp', '_diffrn.ambient_temp_details', '_diffrn.ambient_temp_esd', '_diffrn.crystal_id', '_diffrn.crystal_support', '_diffrn.crystal_treatment', '_diffrn.details', '_diffrn.id', '_diffrn.ambient_pressure', '_diffrn.ambient_pressure_esd', '_diffrn.ambient_pressure_gt', '_diffrn.ambient_pressure_lt', '_diffrn.ambient_temp_gt', '_diffrn.ambient_temp_lt', '_diffrn_detector.details', '_diffrn_detector.detector', '_diffrn_detector.diffrn_id', '_diffrn_detector.type', '_diffrn_detector.area_resol_mean', '_diffrn_detector.dtime', '_diffrn_detector.pdbx_frames_total', '_diffrn_detector.pdbx_collection_time_total', '_diffrn_detector.pdbx_collection_date', '_diffrn_radiation.collimation', '_diffrn_radiation.diffrn_id', '_diffrn_radiation.filter_edge', '_diffrn_radiation.inhomogeneity', '_diffrn_radiation.monochromator', '_diffrn_radiation.polarisn_norm', '_diffrn_radiation.polarisn_ratio', '_diffrn_radiation.probe', '_diffrn_radiation.type', '_diffrn_radiation.xray_symbol', '_diffrn_radiation.wavelength_id', '_diffrn_radiation.pdbx_monochromatic_or_laue_m_l', '_diffrn_radiation.pdbx_wavelength_list', '_diffrn_radiation.pdbx_wavelength', '_diffrn_radiation.pdbx_diffrn_protocol', '_diffrn_radiation.pdbx_analyzer', '_diffrn_radiation.pdbx_scattering_type', '_diffrn_radiation_wavelength.id', '_diffrn_radiation_wavelength.wavelength', '_diffrn_radiation_wavelength.wt', '_diffrn_source.current', '_diffrn_source.details', '_diffrn_source.diffrn_id', '_diffrn_source.power', '_diffrn_source.size', '_diffrn_source.source', '_diffrn_source.target', '_diffrn_source.type', '_diffrn_source.voltage', '_diffrn_source.take-off_angle', '_diffrn_source.pdbx_wavelength_list', '_diffrn_source.pdbx_wavelength', '_diffrn_source.pdbx_synchrotron_beamline', '_diffrn_source.pdbx_synchrotron_site', '_reflns.d_resolution_high', '_reflns.pdbx_number_measured_all', '_reflns.number_obs', '_reflns.pdbx_Rmerge_I_obs', '_reflns.pdbx_netI_over_sigmaI', '_reflns.pdbx_chi_squared', '_reflns.percent_possible_obs', '_reflns.Rmerge_F_obs', '_reflns.observed_criterion_sigma_I', '_reflns.pdbx_Rrim_I_all', '_reflns.B_iso_Wilson_estimate', '_reflns.pdbx_diffrn_id', '_reflns.pdbx_ordinal', '_reflns.entry_id', '_reflns.observed_criterion_sigma_F', '_reflns.d_resolution_low', '_reflns.number_all', '_reflns.pdbx_Rsym_value', '_reflns.pdbx_redundancy', '_reflns_shell.pdbx_diffrn_id', '_reflns_shell.pdbx_ordinal', '_reflns_shell.d_res_high', '_reflns_shell.d_res_low', '_reflns_shell.number_measured_obs', '_reflns_shell.number_measured_all', '_reflns_shell.number_unique_obs', '_reflns_shell.pdbx_rejects', '_reflns_shell.Rmerge_I_obs', '_reflns_shell.meanI_over_sigI_obs', '_reflns_shell.pdbx_Rsym_value', '_reflns_shell.pdbx_chi_squared', '_reflns_shell.pdbx_redundancy', '_reflns_shell.percent_possible_obs', '_reflns_shell.pdbx_netI_over_sigmaI_obs', '_reflns_shell.number_possible', '_reflns_shell.number_unique_all', '_reflns_shell.Rmerge_F_all', '_reflns_shell.Rmerge_F_obs', '_reflns_shell.Rmerge_I_all', '_reflns_shell.meanI_over_sigI_all', '_reflns_shell.percent_possible_all', '_reflns_shell.pdbx_Rrim_I_all', '_reflns_shell.pdbx_Rpim_I_all', '_reflns_shell.pdbx_CC_half', '_refine.entry_id', '_refine.pdbx_refine_id', '_refine.ls_d_res_high', '_refine.ls_d_res_low', '_refine.pdbx_ls_sigma_F', '_refine.pdbx_data_cutoff_high_absF', '_refine.pdbx_data_cutoff_low_absF', '_refine.ls_percent_reflns_obs', '_refine.ls_number_reflns_obs', '_refine.ls_number_reflns_all', '_refine.pdbx_ls_cross_valid_method', '_refine.ls_matrix_type', '_refine.pdbx_R_Free_selection_details', '_refine.details', '_refine.ls_R_factor_all', '_refine.ls_R_factor_obs', '_refine.ls_R_factor_R_work', '_refine.ls_wR_factor_R_work', '_refine.ls_R_factor_R_free', '_refine.ls_wR_factor_R_free', '_refine.ls_percent_reflns_R_free', '_refine.ls_number_reflns_R_free', '_refine.ls_number_reflns_R_work', '_refine.ls_R_factor_R_free_error', '_refine.B_iso_mean', '_refine.solvent_model_param_bsol', '_refine.solvent_model_param_ksol', '_refine.pdbx_isotropic_thermal_model', '_refine.aniso_B[1][1]', '_refine.aniso_B[2][2]', '_refine.aniso_B[3][3]', '_refine.aniso_B[1][2]', '_refine.aniso_B[1][3]', '_refine.aniso_B[2][3]', '_refine.correlation_coeff_Fo_to_Fc', '_refine.correlation_coeff_Fo_to_Fc_free', '_refine.overall_SU_R_Cruickshank_DPI', '_refine.pdbx_overall_SU_R_free_Cruickshank_DPI', '_refine.pdbx_overall_SU_R_Blow_DPI', '_refine.pdbx_overall_SU_R_free_Blow_DPI', '_refine.overall_SU_R_free', '_refine.pdbx_overall_ESU_R', '_refine.pdbx_overall_ESU_R_Free', '_refine.overall_SU_ML', '_refine.overall_SU_B', '_refine.solvent_model_details', '_refine.pdbx_solvent_vdw_probe_radii', '_refine.pdbx_solvent_ion_probe_radii', '_refine.pdbx_solvent_shrinkage_radii', '_refine.ls_number_parameters', '_refine.ls_number_restraints', '_refine.pdbx_starting_model', '_refine.pdbx_method_to_determine_struct', '_refine.pdbx_stereochemistry_target_values', '_refine.pdbx_stereochem_target_val_spec_case', '_refine.overall_FOM_work_R_set', '_refine.B_iso_max', '_refine.B_iso_min', '_refine.pdbx_overall_phase_error', '_refine.occupancy_max', '_refine.occupancy_min', '_refine.pdbx_diffrn_id', '_refine.pdbx_TLS_residual_ADP_flag', '_refine.pdbx_ls_sigma_I', '_refine.pdbx_data_cutoff_high_rms_absF', '_refine.ls_R_factor_R_free_error_details', '_refine_hist.cycle_id', '_refine_hist.pdbx_refine_id', '_refine_hist.d_res_high', '_refine_hist.d_res_low', '_refine_hist.pdbx_number_atoms_ligand', '_refine_hist.number_atoms_solvent', '_refine_hist.number_atoms_total', '_refine_hist.pdbx_number_residues_total', '_refine_hist.pdbx_B_iso_mean_ligand', '_refine_hist.pdbx_B_iso_mean_solvent', '_refine_hist.pdbx_number_atoms_protein', '_refine_hist.pdbx_number_atoms_nucleic_acid', '_refine_ls_restr.pdbx_refine_id', '_refine_ls_restr.type', '_refine_ls_restr.number', '_refine_ls_restr.dev_ideal', '_refine_ls_restr.dev_ideal_target', '_refine_ls_restr.weight', '_refine_ls_restr.pdbx_restraint_function', '_refine_ls_shell.d_res_high', '_refine_ls_shell.d_res_low', '_refine_ls_shell.pdbx_total_number_of_bins_used', '_refine_ls_shell.percent_reflns_obs', '_refine_ls_shell.number_reflns_R_work', '_refine_ls_shell.R_factor_all', '_refine_ls_shell.R_factor_R_work', '_refine_ls_shell.R_factor_R_free', '_refine_ls_shell.percent_reflns_R_free', '_refine_ls_shell.number_reflns_R_free', '_refine_ls_shell.R_factor_R_free_error', '_refine_ls_shell.number_reflns_all', '_refine_ls_shell.number_reflns_obs', '_refine_ls_shell.pdbx_refine_id', '_refine_ls_shell.R_factor_obs', '_struct.entry_id', '_struct.title', '_struct.pdbx_descriptor', '_struct.pdbx_model_details', '_struct.pdbx_formula_weight', '_struct.pdbx_formula_weight_method', '_struct.pdbx_model_type_details', '_struct.pdbx_CASP_flag', '_struct_keywords.entry_id', '_struct_keywords.text', '_struct_keywords.pdbx_keywords', '_struct_asym.id', '_struct_asym.pdbx_blank_PDB_chainid_flag', '_struct_asym.pdbx_modified', '_struct_asym.entity_id', '_struct_asym.details', '_struct_conf.conf_type_id', '_struct_conf.id', '_struct_conf.pdbx_PDB_helix_id', '_struct_conf.beg_label_comp_id', '_struct_conf.beg_label_asym_id', '_struct_conf.beg_label_seq_id', '_struct_conf.pdbx_beg_PDB_ins_code', '_struct_conf.end_label_comp_id', '_struct_conf.end_label_asym_id', '_struct_conf.end_label_seq_id', '_struct_conf.pdbx_end_PDB_ins_code', '_struct_conf.beg_auth_comp_id', '_struct_conf.beg_auth_asym_id', '_struct_conf.beg_auth_seq_id', '_struct_conf.end_auth_comp_id', '_struct_conf.end_auth_asym_id', '_struct_conf.end_auth_seq_id', '_struct_conf.pdbx_PDB_helix_class', '_struct_conf.details', '_struct_conf.pdbx_PDB_helix_length', '_struct_conf_type.id', '_struct_conf_type.criteria', '_struct_conf_type.reference', '_struct_conn.id', '_struct_conn.conn_type_id', '_struct_conn.pdbx_leaving_atom_flag', '_struct_conn.pdbx_PDB_id', '_struct_conn.ptnr1_label_asym_id', '_struct_conn.ptnr1_label_comp_id', '_struct_conn.ptnr1_label_seq_id', '_struct_conn.ptnr1_label_atom_id', '_struct_conn.pdbx_ptnr1_label_alt_id', '_struct_conn.pdbx_ptnr1_PDB_ins_code', '_struct_conn.pdbx_ptnr1_standard_comp_id', '_struct_conn.ptnr1_symmetry', '_struct_conn.ptnr2_label_asym_id', '_struct_conn.ptnr2_label_comp_id', '_struct_conn.ptnr2_label_seq_id', '_struct_conn.ptnr2_label_atom_id', '_struct_conn.pdbx_ptnr2_label_alt_id', '_struct_conn.pdbx_ptnr2_PDB_ins_code', '_struct_conn.ptnr1_auth_asym_id', '_struct_conn.ptnr1_auth_comp_id', '_struct_conn.ptnr1_auth_seq_id', '_struct_conn.ptnr2_auth_asym_id', '_struct_conn.ptnr2_auth_comp_id', '_struct_conn.ptnr2_auth_seq_id', '_struct_conn.ptnr2_symmetry', '_struct_conn.pdbx_ptnr3_label_atom_id', '_struct_conn.pdbx_ptnr3_label_seq_id', '_struct_conn.pdbx_ptnr3_label_comp_id', '_struct_conn.pdbx_ptnr3_label_asym_id', '_struct_conn.pdbx_ptnr3_label_alt_id', '_struct_conn.pdbx_ptnr3_PDB_ins_code', '_struct_conn.details', '_struct_conn.pdbx_dist_value', '_struct_conn.pdbx_value_order', '_struct_conn_type.id', '_struct_conn_type.criteria', '_struct_conn_type.reference', '_struct_mon_prot_cis.pdbx_id', '_struct_mon_prot_cis.label_comp_id', '_struct_mon_prot_cis.label_seq_id', '_struct_mon_prot_cis.label_asym_id', '_struct_mon_prot_cis.label_alt_id', '_struct_mon_prot_cis.pdbx_PDB_ins_code', '_struct_mon_prot_cis.auth_comp_id', '_struct_mon_prot_cis.auth_seq_id', '_struct_mon_prot_cis.auth_asym_id', '_struct_mon_prot_cis.pdbx_label_comp_id_2', '_struct_mon_prot_cis.pdbx_label_seq_id_2', '_struct_mon_prot_cis.pdbx_label_asym_id_2', '_struct_mon_prot_cis.pdbx_PDB_ins_code_2', '_struct_mon_prot_cis.pdbx_auth_comp_id_2', '_struct_mon_prot_cis.pdbx_auth_seq_id_2', '_struct_mon_prot_cis.pdbx_auth_asym_id_2', '_struct_mon_prot_cis.pdbx_PDB_model_num', '_struct_mon_prot_cis.pdbx_omega_angle', '_struct_sheet.id', '_struct_sheet.type', '_struct_sheet.number_strands', '_struct_sheet.details', '_struct_sheet_order.sheet_id', '_struct_sheet_order.range_id_1', '_struct_sheet_order.range_id_2', '_struct_sheet_order.offset', '_struct_sheet_order.sense', '_struct_sheet_range.sheet_id', '_struct_sheet_range.id', '_struct_sheet_range.beg_label_comp_id', '_struct_sheet_range.beg_label_asym_id', '_struct_sheet_range.beg_label_seq_id', '_struct_sheet_range.pdbx_beg_PDB_ins_code', '_struct_sheet_range.end_label_comp_id', '_struct_sheet_range.end_label_asym_id', '_struct_sheet_range.end_label_seq_id', '_struct_sheet_range.pdbx_end_PDB_ins_code', '_struct_sheet_range.beg_auth_comp_id', '_struct_sheet_range.beg_auth_asym_id', '_struct_sheet_range.beg_auth_seq_id', '_struct_sheet_range.end_auth_comp_id', '_struct_sheet_range.end_auth_asym_id', '_struct_sheet_range.end_auth_seq_id', '_pdbx_struct_sheet_hbond.sheet_id', '_pdbx_struct_sheet_hbond.range_id_1', '_pdbx_struct_sheet_hbond.range_id_2', '_pdbx_struct_sheet_hbond.range_1_label_atom_id', '_pdbx_struct_sheet_hbond.range_1_label_comp_id', '_pdbx_struct_sheet_hbond.range_1_label_asym_id', '_pdbx_struct_sheet_hbond.range_1_label_seq_id', '_pdbx_struct_sheet_hbond.range_1_PDB_ins_code', '_pdbx_struct_sheet_hbond.range_1_auth_atom_id', '_pdbx_struct_sheet_hbond.range_1_auth_comp_id', '_pdbx_struct_sheet_hbond.range_1_auth_asym_id', '_pdbx_struct_sheet_hbond.range_1_auth_seq_id', '_pdbx_struct_sheet_hbond.range_2_label_atom_id', '_pdbx_struct_sheet_hbond.range_2_label_comp_id', '_pdbx_struct_sheet_hbond.range_2_label_asym_id', '_pdbx_struct_sheet_hbond.range_2_label_seq_id', '_pdbx_struct_sheet_hbond.range_2_PDB_ins_code', '_pdbx_struct_sheet_hbond.range_2_auth_atom_id', '_pdbx_struct_sheet_hbond.range_2_auth_comp_id', '_pdbx_struct_sheet_hbond.range_2_auth_asym_id', '_pdbx_struct_sheet_hbond.range_2_auth_seq_id', '_struct_site.id', '_struct_site.pdbx_evidence_code', '_struct_site.pdbx_auth_asym_id', '_struct_site.pdbx_auth_comp_id', '_struct_site.pdbx_auth_seq_id', '_struct_site.pdbx_auth_ins_code', '_struct_site.pdbx_num_residues', '_struct_site.details', '_struct_site_gen.id', '_struct_site_gen.site_id', '_struct_site_gen.pdbx_num_res', '_struct_site_gen.label_comp_id', '_struct_site_gen.label_asym_id', '_struct_site_gen.label_seq_id', '_struct_site_gen.pdbx_auth_ins_code', '_struct_site_gen.auth_comp_id', '_struct_site_gen.auth_asym_id', '_struct_site_gen.auth_seq_id', '_struct_site_gen.label_atom_id', '_struct_site_gen.label_alt_id', '_struct_site_gen.symmetry', '_struct_site_gen.details', '_atom_sites.entry_id', '_atom_sites.fract_transf_matrix[1][1]', '_atom_sites.fract_transf_matrix[1][2]', '_atom_sites.fract_transf_matrix[1][3]', '_atom_sites.fract_transf_matrix[2][1]', '_atom_sites.fract_transf_matrix[2][2]', '_atom_sites.fract_transf_matrix[2][3]', '_atom_sites.fract_transf_matrix[3][1]', '_atom_sites.fract_transf_matrix[3][2]', '_atom_sites.fract_transf_matrix[3][3]', '_atom_sites.fract_transf_vector[1]', '_atom_sites.fract_transf_vector[2]', '_atom_sites.fract_transf_vector[3]', '_atom_type.symbol', '_atom_site.group_PDB', '_atom_site.id', '_atom_site.type_symbol', '_atom_site.label_atom_id', '_atom_site.label_alt_id', '_atom_site.label_comp_id', '_atom_site.label_asym_id', '_atom_site.label_entity_id', '_atom_site.label_seq_id', '_atom_site.pdbx_PDB_ins_code', '_atom_site.Cartn_x', '_atom_site.Cartn_y', '_atom_site.Cartn_z', '_atom_site.occupancy', '_atom_site.B_iso_or_equiv', '_atom_site.pdbx_formal_charge', '_atom_site.auth_seq_id', '_atom_site.auth_comp_id', '_atom_site.auth_asym_id', '_atom_site.auth_atom_id', '_atom_site.pdbx_PDB_model_num', '_pdbx_poly_seq_scheme.asym_id', '_pdbx_poly_seq_scheme.entity_id', '_pdbx_poly_seq_scheme.seq_id', '_pdbx_poly_seq_scheme.mon_id', '_pdbx_poly_seq_scheme.ndb_seq_num', '_pdbx_poly_seq_scheme.pdb_seq_num', '_pdbx_poly_seq_scheme.auth_seq_num', '_pdbx_poly_seq_scheme.pdb_mon_id', '_pdbx_poly_seq_scheme.auth_mon_id', '_pdbx_poly_seq_scheme.pdb_strand_id', '_pdbx_poly_seq_scheme.pdb_ins_code', '_pdbx_poly_seq_scheme.hetero', '_pdbx_nonpoly_scheme.asym_id', '_pdbx_nonpoly_scheme.entity_id', '_pdbx_nonpoly_scheme.mon_id', '_pdbx_nonpoly_scheme.ndb_seq_num', '_pdbx_nonpoly_scheme.pdb_seq_num', '_pdbx_nonpoly_scheme.auth_seq_num', '_pdbx_nonpoly_scheme.pdb_mon_id', '_pdbx_nonpoly_scheme.auth_mon_id', '_pdbx_nonpoly_scheme.pdb_strand_id', '_pdbx_nonpoly_scheme.pdb_ins_code', '_pdbx_struct_assembly.id', '_pdbx_struct_assembly.details', '_pdbx_struct_assembly.method_details', '_pdbx_struct_assembly.oligomeric_details', '_pdbx_struct_assembly.oligomeric_count', '_pdbx_struct_assembly_gen.assembly_id', '_pdbx_struct_assembly_gen.oper_expression', '_pdbx_struct_assembly_gen.asym_id_list', '_pdbx_struct_oper_list.id', '_pdbx_struct_oper_list.type', '_pdbx_struct_oper_list.name', '_pdbx_struct_oper_list.symmetry_operation', '_pdbx_struct_oper_list.matrix[1][1]', '_pdbx_struct_oper_list.matrix[1][2]', '_pdbx_struct_oper_list.matrix[1][3]', '_pdbx_struct_oper_list.vector[1]', '_pdbx_struct_oper_list.matrix[2][1]', '_pdbx_struct_oper_list.matrix[2][2]', '_pdbx_struct_oper_list.matrix[2][3]', '_pdbx_struct_oper_list.vector[2]', '_pdbx_struct_oper_list.matrix[3][1]', '_pdbx_struct_oper_list.matrix[3][2]', '_pdbx_struct_oper_list.matrix[3][3]', '_pdbx_struct_oper_list.vector[3]', '_pdbx_struct_conn_angle.id', '_pdbx_struct_conn_angle.ptnr1_label_atom_id', '_pdbx_struct_conn_angle.ptnr1_label_alt_id', '_pdbx_struct_conn_angle.ptnr1_label_asym_id', '_pdbx_struct_conn_angle.ptnr1_label_comp_id', '_pdbx_struct_conn_angle.ptnr1_label_seq_id', '_pdbx_struct_conn_angle.ptnr1_auth_atom_id', '_pdbx_struct_conn_angle.ptnr1_auth_asym_id', '_pdbx_struct_conn_angle.ptnr1_auth_comp_id', '_pdbx_struct_conn_angle.ptnr1_auth_seq_id', '_pdbx_struct_conn_angle.ptnr1_PDB_ins_code', '_pdbx_struct_conn_angle.ptnr1_symmetry', '_pdbx_struct_conn_angle.ptnr2_label_atom_id', '_pdbx_struct_conn_angle.ptnr2_label_alt_id', '_pdbx_struct_conn_angle.ptnr2_label_asym_id', '_pdbx_struct_conn_angle.ptnr2_label_comp_id', '_pdbx_struct_conn_angle.ptnr2_label_seq_id', '_pdbx_struct_conn_angle.ptnr2_auth_atom_id', '_pdbx_struct_conn_angle.ptnr2_auth_asym_id', '_pdbx_struct_conn_angle.ptnr2_auth_comp_id', '_pdbx_struct_conn_angle.ptnr2_auth_seq_id', '_pdbx_struct_conn_angle.ptnr2_PDB_ins_code', '_pdbx_struct_conn_angle.ptnr2_symmetry', '_pdbx_struct_conn_angle.ptnr3_label_atom_id', '_pdbx_struct_conn_angle.ptnr3_label_alt_id', '_pdbx_struct_conn_angle.ptnr3_label_asym_id', '_pdbx_struct_conn_angle.ptnr3_label_comp_id', '_pdbx_struct_conn_angle.ptnr3_label_seq_id', '_pdbx_struct_conn_angle.ptnr3_auth_atom_id', '_pdbx_struct_conn_angle.ptnr3_auth_asym_id', '_pdbx_struct_conn_angle.ptnr3_auth_comp_id', '_pdbx_struct_conn_angle.ptnr3_auth_seq_id', '_pdbx_struct_conn_angle.ptnr3_PDB_ins_code', '_pdbx_struct_conn_angle.ptnr3_symmetry', '_pdbx_struct_conn_angle.value', '_pdbx_struct_conn_angle.value_esd', '_pdbx_audit_revision_history.ordinal', '_pdbx_audit_revision_history.data_content_type', '_pdbx_audit_revision_history.major_revision', '_pdbx_audit_revision_history.minor_revision', '_pdbx_audit_revision_history.revision_date', '_pdbx_audit_revision_details.ordinal', '_pdbx_audit_revision_details.revision_ordinal', '_pdbx_audit_revision_details.data_content_type', '_pdbx_audit_revision_details.provider', '_pdbx_audit_revision_details.type', '_pdbx_audit_revision_details.description', '_pdbx_audit_revision_group.ordinal', '_pdbx_audit_revision_group.revision_ordinal', '_pdbx_audit_revision_group.data_content_type', '_pdbx_audit_revision_group.group', '_software.citation_id', '_software.classification', '_software.compiler_name', '_software.compiler_version', '_software.contact_author', '_software.contact_author_email', '_software.date', '_software.description', '_software.dependencies', '_software.hardware', '_software.language', '_software.location', '_software.mods', '_software.name', '_software.os', '_software.os_version', '_software.type', '_software.version', '_software.pdbx_ordinal', '_pdbx_validate_close_contact.id', '_pdbx_validate_close_contact.PDB_model_num', '_pdbx_validate_close_contact.auth_atom_id_1', '_pdbx_validate_close_contact.auth_asym_id_1', '_pdbx_validate_close_contact.auth_comp_id_1', '_pdbx_validate_close_contact.auth_seq_id_1', '_pdbx_validate_close_contact.PDB_ins_code_1', '_pdbx_validate_close_contact.label_alt_id_1', '_pdbx_validate_close_contact.auth_atom_id_2', '_pdbx_validate_close_contact.auth_asym_id_2', '_pdbx_validate_close_contact.auth_comp_id_2', '_pdbx_validate_close_contact.auth_seq_id_2', '_pdbx_validate_close_contact.PDB_ins_code_2', '_pdbx_validate_close_contact.label_alt_id_2', '_pdbx_validate_close_contact.dist', '_pdbx_validate_torsion.id', '_pdbx_validate_torsion.PDB_model_num', '_pdbx_validate_torsion.auth_comp_id', '_pdbx_validate_torsion.auth_asym_id', '_pdbx_validate_torsion.auth_seq_id', '_pdbx_validate_torsion.PDB_ins_code', '_pdbx_validate_torsion.label_alt_id', '_pdbx_validate_torsion.phi', '_pdbx_validate_torsion.psi', '_pdbx_validate_peptide_omega.id', '_pdbx_validate_peptide_omega.PDB_model_num', '_pdbx_validate_peptide_omega.auth_comp_id_1', '_pdbx_validate_peptide_omega.auth_asym_id_1', '_pdbx_validate_peptide_omega.auth_seq_id_1', '_pdbx_validate_peptide_omega.PDB_ins_code_1', '_pdbx_validate_peptide_omega.label_alt_id_1', '_pdbx_validate_peptide_omega.auth_comp_id_2', '_pdbx_validate_peptide_omega.auth_asym_id_2', '_pdbx_validate_peptide_omega.auth_seq_id_2', '_pdbx_validate_peptide_omega.PDB_ins_code_2', '_pdbx_validate_peptide_omega.label_alt_id_2', '_pdbx_validate_peptide_omega.omega', '_pdbx_unobs_or_zero_occ_atoms.id', '_pdbx_unobs_or_zero_occ_atoms.PDB_model_num', '_pdbx_unobs_or_zero_occ_atoms.polymer_flag', '_pdbx_unobs_or_zero_occ_atoms.occupancy_flag', '_pdbx_unobs_or_zero_occ_atoms.auth_asym_id', '_pdbx_unobs_or_zero_occ_atoms.auth_comp_id', '_pdbx_unobs_or_zero_occ_atoms.auth_seq_id', '_pdbx_unobs_or_zero_occ_atoms.PDB_ins_code', '_pdbx_unobs_or_zero_occ_atoms.auth_atom_id', '_pdbx_unobs_or_zero_occ_atoms.label_alt_id', '_pdbx_unobs_or_zero_occ_atoms.label_asym_id', '_pdbx_unobs_or_zero_occ_atoms.label_comp_id', '_pdbx_unobs_or_zero_occ_atoms.label_seq_id', '_pdbx_unobs_or_zero_occ_atoms.label_atom_id', '_pdbx_entity_nonpoly.entity_id', '_pdbx_entity_nonpoly.name', '_pdbx_entity_nonpoly.comp_id'])
As you can see we have tons of keys.
Binding sites are often annotated by the researches in their mmCIF files.
loop_
_struct_site.id
_struct_site.pdbx_evidence_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_struct_site.pdbx_auth_ins_code
_struct_site.pdbx_num_residues
_struct_site.details
AC1 Software A NA 701 ? 5 'binding site for residue NA A 701'
AC2 Software A NA 702 ? 5 'binding site for residue NA A 702'
AC3 Software A CL 703 ? 4 'binding site for residue CL A 703'
AC4 Software A MAL 704 ? 4 'binding site for residue MAL A 704'
AC5 Software A MAL 705 ? 4 'binding site for residue MAL A 705'
AC6 Software A P4G 707 ? 1 'binding site for residue P4G A 707'
AC7 Software A LDP 708 ? 9 'binding site for residue LDP A 708'
AC8 Software A EDO 709 ? 2 'binding site for residue EDO A 709'
AC9 Software A Y01 710 ? 4 'binding site for residue Y01 A 710'
AD1 Software A CLR 711 ? 5 'binding site for residue CLR A 711'
AD2 Software L NA 301 ? 4 'binding site for residue NA L 301'
AD3 Software A NAG 706 ? 1 'binding site for Mono-Saccharide NAG A 706 bound to ASN A 141'
struc_dict['_struct_site.details']
['binding site for residue NA A 701', 'binding site for residue NA A 702', 'binding site for residue CL A 703', 'binding site for residue MAL A 704', 'binding site for residue MAL A 705', 'binding site for residue P4G A 707', 'binding site for residue LDP A 708', 'binding site for residue EDO A 709', 'binding site for residue Y01 A 710', 'binding site for residue CLR A 711', 'binding site for residue NA L 301', 'binding site for Mono-Saccharide NAG A 706 bound to ASN A 141']
So the binding site for LDP has ID AC7
.
Now if we look at another entry in the mmCIF we can get a list of all the residues in each binding site:
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 5 ALA A 20 ? ALA A 44 . ? 1_555 ?
2 AC1 5 ASN A 25 ? ASN A 49 . ? 1_555 ?
3 AC1 5 SER A 255 ? SER A 320 . ? 1_555 ?
4 AC1 5 ASN A 287 ? ASN A 352 . ? 1_555 ?
5 AC1 5 HOH P . ? HOH A 814 . ? 1_555 ?
...
...
There are other useful entries such as the title of the publication that this structure was featured in.
struc_dict['_citation.title']
'Neurotransmitter and psychostimulant recognition by the dopamine transporter.'
All entry types are documented here.
Let's extract all residues in the LDP binding site.
site_ID = struc_dict['_struct_site_gen.site_id']
site_chain = struc_dict['_struct_site_gen.auth_asym_id']
site_resnum = struc_dict['_struct_site_gen.auth_seq_id']
site_resname = struc_dict['_struct_site_gen.label_comp_id']
cif_binding_residues = []
for bind_id, ch, num, name in zip(site_ID, site_chain, site_resnum, site_resname):
if bind_id == "AC7":
print(bind_id, ch, num, name)
try:
cif_binding_residues.append(structure[0][ch][int(num)])
except:
continue
else:
continue
AC7 A 46 ASP AC7 A 117 ALA AC7 A 120 VAL AC7 A 121 ASP AC7 A 124 TYR AC7 A 325 PHE AC7 A 422 SER AC7 A 425 GLY AC7 A 812 HOH
Let's say we don't trust this annotation. We can compute our own ligand binding site and compare.
NOTE: Obviously we could have done this directly with the structure
object we obtained earlier.
We can get all the residues of a model using the model.get_residues()
method.
#finding LDP residue
LDP = None
for res in structure[0].get_residues():
if res.resname == "LDP":
LDP = res
break
print(LDP)
<Residue LDP het=H_LDP resseq=708 icode= >
Let's set a distance cutoff of 10 Angstroms.
We will count as binding residues any residue whose $\alpha$-carbon is within 10 Angstrom of any atom in LDP.
BioPython gives us a vector of X, Y, Z coordinates for every atom in the residue.
Let's get the X, Y, Z coordinates of the alpha carbon of residue 56 in chain A.
For this, we use the coord
attribute.
res_1_CA = structure[0]['A'][56]['CA']
print(res_1_CA.coord)
[ 3.7650001 -10.38899994 -31.97200012]
Now we can use this to compute distances!
Let's take another atom.
res_2_CA = structure[0]['A'][327]['CA']
print(res_2_CA.coord)
[-12.76200008 9.25 -31.8939991 ]
The difference between the coordinates will be a 3D vector.
diff = res_1_CA.coord - res_2_CA.coord
print(diff)
[ 16.52700043 -19.63899994 -0.07800102]
To get positive values we square the vector and then take the square root.
import numpy as np
dist = np.sqrt(diff * diff)
print(dist)
[ 16.52700043 19.63899994 0.07800102]
We now have the distance along each axis between the two CA atoms of the two residues.
We can apply this to every residue.
cutoff = 10
binding_residues = []
for res in structure[0].get_residues():
#skip the LDP residue
if res == LDP:
continue
#non-amino acid residues are tagged with an 'H' in their id tuple
#we want to skip these
elif res.id[0].startswith("H"):
continue
else:
alpha_carbon = res['CA']
distances = []
for atom in LDP:
#subtract the two position vectors
diff_vector = alpha_carbon.coord - atom.coord
#to get a positive value we square the difference vector
#we then take the square root to go back to the original scale
distances.append(np.sqrt(np.sum(diff_vector * diff_vector)))
#we get the nearest atom using min(distances) and see if it falls inside
#the cutoff
if min(distances) < cutoff:
binding_residues.append(res)
print(binding_residues)
[<Residue GLY het= resseq=42 icode= >, <Residue PHE het= resseq=43 icode= >, <Residue ALA het= resseq=44 icode= >, <Residue VAL het= resseq=45 icode= >, <Residue ASP het= resseq=46 icode= >, <Residue LEU het= resseq=47 icode= >, <Residue ALA het= resseq=48 icode= >, <Residue ASN het= resseq=49 icode= >, <Residue VAL het= resseq=113 icode= >, <Residue VAL het= resseq=114 icode= >, <Residue LEU het= resseq=115 icode= >, <Residue ILE het= resseq=116 icode= >, <Residue ALA het= resseq=117 icode= >, <Residue PHE het= resseq=118 icode= >, <Residue TYR het= resseq=119 icode= >, <Residue VAL het= resseq=120 icode= >, <Residue ASP het= resseq=121 icode= >, <Residue PHE het= resseq=122 icode= >, <Residue TYR het= resseq=123 icode= >, <Residue TYR het= resseq=124 icode= >, <Residue ASN het= resseq=125 icode= >, <Residue VAL het= resseq=126 icode= >, <Residue ILE het= resseq=127 icode= >, <Residue ILE het= resseq=128 icode= >, <Residue CYS het= resseq=250 icode= >, <Residue PHE het= resseq=319 icode= >, <Residue SER het= resseq=320 icode= >, <Residue LEU het= resseq=321 icode= >, <Residue GLY het= resseq=322 icode= >, <Residue PRO het= resseq=323 icode= >, <Residue GLY het= resseq=324 icode= >, <Residue PHE het= resseq=325 icode= >, <Residue GLY het= resseq=326 icode= >, <Residue VAL het= resseq=327 icode= >, <Residue LEU het= resseq=328 icode= >, <Residue LEU het= resseq=417 icode= >, <Residue GLY het= resseq=418 icode= >, <Residue LEU het= resseq=419 icode= >, <Residue ASP het= resseq=420 icode= >, <Residue SER het= resseq=421 icode= >, <Residue SER het= resseq=422 icode= >, <Residue PHE het= resseq=423 icode= >, <Residue GLY het= resseq=424 icode= >, <Residue GLY het= resseq=425 icode= >, <Residue SER het= resseq=426 icode= >, <Residue GLU het= resseq=427 icode= >, <Residue ALA het= resseq=428 icode= >, <Residue ILE het= resseq=429 icode= >, <Residue TYR het= resseq=455 icode= >, <Residue ASP het= resseq=475 icode= >, <Residue ALA het= resseq=478 icode= >, <Residue ALA het= resseq=479 icode= >, <Residue ILE het= resseq=483 icode= >]
#view = nv.demo()
view = nv.show_biopython(structure)
# use hex values for now.
residues = structure[0].get_residues()
#this is a bit of a hack to set the binding residues to red in the visualization
colors = ['0x0000FF' if r not in binding_residues else '0xFF0000' for r in residues]
view._set_color_by_residue(colors, component_index=0, repr_index=0)
view
A Jupyter Widget
Ok now let's compare this to our list of residues obtained from the mmCIF annotations.
view = nv.show_biopython(structure)
# use hex values for now.
residues = structure[0].get_residues()
#this is a bit of a hack to set the binding residues to red in the visualization
colors = ['0x0000FF' if r not in cif_binding_residues else '0xFF0000' for r in residues]
view._set_color_by_residue(colors, component_index=0, repr_index=0)
view
A Jupyter Widget
It looks like we were maybe a bit too permissive with our distance cutoff.