COMP 364: Molecular Structures with BioPython

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.

What is a structure?

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

Downloading a Structure File from the 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.

In [1]:
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
Out[1]:
'/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.

In [2]:
import os
os.listdir()
Out[2]:
['.ipynb_checkpoints', '4xp1.cif', 'L27.ipynb', 'obsolete', 'xp']
In [3]:
os.listdir('xp')
Out[3]:
['4xp1.cif']

Parsing Structure files

In [4]:
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.

In [5]:
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.

In [6]:
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.

Visualizing structures in jupyter Notebooks

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.

In [7]:
import nglview as nv
In [8]:
view = nv.show_biopython(structure)
view.clear_representations()
#view as ball and stick (atom and bond)
view.add_ball_and_stick()
In [9]:
view

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.

In [10]:
view.clear_representations()
#add ribbons
view.add_cartoon('protein')
#add ball and stick for non-rotien
view.add_ball_and_stick('not protein')
view

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.

In [11]:
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.

In [12]:
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.

In [13]:
chain_A = model['A']
In [14]:
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.

In [15]:
res = chain_A[56]
In [16]:
print(res)
<Residue LEU het=  resseq=56 icode= >
In [17]:
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.

In [18]:
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>
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<Atom O>

Mini project: find the dopamine binding pockets

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 annotations

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.

In [19]:
struc_dict = MMCIF2Dict.MMCIF2Dict('xp/4xp1.cif')
In [20]:
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'
In [21]:
struc_dict['_struct_site.details']
Out[21]:
['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.

In [22]:
struc_dict['_citation.title']
Out[22]:
'Neurotransmitter and psychostimulant recognition by the dopamine transporter.'

All entry types are documented here.

Let's extract all residues in the LDP binding site.

In [23]:
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.

Step 1: Find the LDP residue

We can get all the residues of a model using the model.get_residues() method.

In [24]:
#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= >

Step 2: find all other residues within a certain distance cutoff

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.

In [25]:
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.

In [32]:
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.

In [28]:
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.

In [29]:
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.

In [38]:
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)
In [39]:
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= >]
In [40]:
#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

Ok now let's compare this to our list of residues obtained from the mmCIF annotations.

In [41]:
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

It looks like we were maybe a bit too permissive with our distance cutoff.