Step 1
In pDynamo, PDB files can be read and converted directly to systems using the function PDBFile_ToSystem. This is illustrated by Examples 2 and 19 of the pDynamo distribution, Unfortunately, the function often fails with many PDB files, including those containing experimental structures, or it generates systems of incorrect composition. When this is so, the solution is to convert the information on the PDB file into a PDB model which can then be modified as appropriate.
PDB files can be read and converted to PDB models using the function PDBFile_ToPDBModel and the model written out to a PDB model file with the function PDBModelFile_FromPDBModel. Suitable commands to do this for the file 1CDK.pdb are:
# . Read the PDB file and create a PDB model.
model = PDBFile_ToPDBModel ( "1CDK.pdb" )
model.Summary ( )
# . Write out the PDB model.
PDBModelFile_FromPDBModel ( "1CDK.model", model )
The file 1CDK.pdb is read successfully although there are some warnings which, in this case, can be ignored. The model file that is produced is listed below (some parts have been omitted for brevity):
PDBModel Camp-Dependent Protein Kinase Catalytic Subunit(E.C.2.7.1.37) (Protein Kinase A)
Chain A
497
LYS:8 ; GLY:9 ; SER:10 ; GLU:11 ; GLN:12 ; GLU:13 ; SER:14 ; VAL:15 ; LYS:16 ; GLU:17
PHE:18 ; LEU:19 ; ALA:20 ; LYS:21 ; ALA:22 ; LYS:23 ; GLU:24 ; ASP:25 ; PHE:26 ; LEU:27
LYS:28 ; LYS:29 ; TRP:30 ; GLU:31 ; ASN:32 ; PRO:33 ; ALA:34 ; GLN:35 ; ASN:36 ; THR:37
ALA:38 ; HIS:39 ; LEU:40 ; ASP:41 ; GLN:42 ; PHE:43 ; GLU:44 ; ARG:45 ; ILE:46 ; LYS:47
THR:48 ; LEU:49 ; GLY:50 ; THR:51 ; GLY:52 ; SER:53 ; PHE:54 ; GLY:55 ; ARG:56 ; VAL:57
MET:58 ; LEU:59 ; VAL:60 ; LYS:61 ; HIS:62 ; LYS:63 ; GLU:64 ; THR:65 ; GLY:66 ; ASN:67
HIS:68 ; PHE:69 ; ALA:70 ; MET:71 ; LYS:72 ; ILE:73 ; LEU:74 ; ASP:75 ; LYS:76 ; GLN:77
LYS:78 ; VAL:79 ; VAL:80 ; LYS:81 ; LEU:82 ; LYS:83 ; GLN:84 ; ILE:85 ; GLU:86 ; HIS:87
THR:88 ; LEU:89 ; ASN:90 ; GLU:91 ; LYS:92 ; ARG:93 ; ILE:94 ; LEU:95 ; GLN:96 ; ALA:97
VAL:98 ; ASN:99 ; PHE:100 ; PRO:101 ; PHE:102 ; LEU:103 ; VAL:104 ; LYS:105 ; LEU:106 ; GLU:107
TYR:108 ; SER:109 ; PHE:110 ; LYS:111 ; ASP:112 ; ASN:113 ; SER:114 ; ASN:115 ; LEU:116 ; TYR:117
MET:118 ; VAL:119 ; MET:120 ; GLU:121 ; TYR:122 ; VAL:123 ; PRO:124 ; GLY:125 ; GLY:126 ; GLU:127
MET:128 ; PHE:129 ; SER:130 ; HIS:131 ; LEU:132 ; ARG:133 ; ARG:134 ; ILE:135 ; GLY:136 ; ARG:137
PHE:138 ; SER:139 ; GLU:140 ; PRO:141 ; HIS:142 ; ALA:143 ; ARG:144 ; PHE:145 ; TYR:146 ; ALA:147
ALA:148 ; GLN:149 ; ILE:150 ; VAL:151 ; LEU:152 ; THR:153 ; PHE:154 ; GLU:155 ; TYR:156 ; LEU:157
HIS:158 ; SER:159 ; LEU:160 ; ASP:161 ; LEU:162 ; ILE:163 ; TYR:164 ; ARG:165 ; ASP:166 ; LEU:167
LYS:168 ; PRO:169 ; GLU:170 ; ASN:171 ; LEU:172 ; LEU:173 ; ILE:174 ; ASP:175 ; GLN:176 ; GLN:177
GLY:178 ; TYR:179 ; ILE:180 ; GLN:181 ; VAL:182 ; THR:183 ; ASP:184 ; PHE:185 ; GLY:186 ; PHE:187
ALA:188 ; LYS:189 ; ARG:190 ; VAL:191 ; LYS:192 ; GLY:193 ; ARG:194 ; THR:195 ; TRP:196 ; THR:197
LEU:198 ; CYS:199 ; GLY:200 ; THR:201 ; PRO:202 ; GLU:203 ; TYR:204 ; LEU:205 ; ALA:206 ; PRO:207
GLU:208 ; ILE:209 ; ILE:210 ; LEU:211 ; SER:212 ; LYS:213 ; GLY:214 ; TYR:215 ; ASN:216 ; LYS:217
ALA:218 ; VAL:219 ; ASP:220 ; TRP:221 ; TRP:222 ; ALA:223 ; LEU:224 ; GLY:225 ; VAL:226 ; LEU:227
ILE:228 ; TYR:229 ; GLU:230 ; MET:231 ; ALA:232 ; ALA:233 ; GLY:234 ; TYR:235 ; PRO:236 ; PRO:237
PHE:238 ; PHE:239 ; ALA:240 ; ASP:241 ; GLN:242 ; PRO:243 ; ILE:244 ; GLN:245 ; ILE:246 ; TYR:247
GLU:248 ; LYS:249 ; ILE:250 ; VAL:251 ; SER:252 ; GLY:253 ; LYS:254 ; VAL:255 ; ARG:256 ; PHE:257
PRO:258 ; SER:259 ; HIS:260 ; PHE:261 ; SER:262 ; SER:263 ; ASP:264 ; LEU:265 ; LYS:266 ; ASP:267
LEU:268 ; LEU:269 ; ARG:270 ; ASN:271 ; LEU:272 ; LEU:273 ; GLN:274 ; VAL:275 ; ASP:276 ; LEU:277
THR:278 ; LYS:279 ; ARG:280 ; PHE:281 ; GLY:282 ; ASN:283 ; LEU:284 ; LYS:285 ; ASP:286 ; GLY:287
VAL:288 ; ASN:289 ; ASP:290 ; ILE:291 ; LYS:292 ; ASN:293 ; HIS:294 ; LYS:295 ; TRP:296 ; PHE:297
ALA:298 ; THR:299 ; THR:300 ; ASP:301 ; TRP:302 ; ILE:303 ; ALA:304 ; ILE:305 ; TYR:306 ; GLN:307
ARG:308 ; LYS:309 ; VAL:310 ; GLU:311 ; ALA:312 ; PRO:313 ; PHE:314 ; ILE:315 ; PRO:316 ; LYS:317
PHE:318 ; LYS:319 ; GLY:320 ; PRO:321 ; GLY:322 ; ASP:323 ; THR:324 ; SER:325 ; ASN:326 ; PHE:327
ASP:328 ; ASP:329 ; TYR:330 ; GLU:331 ; GLU:332 ; GLU:333 ; GLU:334 ; ILE:335 ; ARG:336 ; VAL:337
SER:338 ; ILE:339 ; ASN:340 ; GLU:341 ; LYS:342 ; CYS:343 ; GLY:344 ; LYS:345 ; GLU:346 ; PHE:347
SER:348 ; GLU:349 ; PHE:350 ; PO3:197 ; ANP:400 ; MN:401 ; MN:402 ; MYR:403 ; HOH:500 ; HOH:501
HOH:502 ; HOH:504 ; HOH:505 ; HOH:506 ; HOH:507 ; HOH:508 ; HOH:509 ; HOH:510 ; HOH:512 ; HOH:513
HOH:514 ; HOH:515 ; HOH:516 ; HOH:518 ; HOH:519 ; HOH:520 ; HOH:521 ; HOH:522 ; HOH:523 ; HOH:524
HOH:525 ; HOH:526 ; HOH:527 ; HOH:528 ; HOH:530 ; HOH:531 ; HOH:532 ; HOH:533 ; HOH:534 ; HOH:535
HOH:536 ; HOH:537 ; HOH:538 ; HOH:539 ; HOH:540 ; HOH:541 ; HOH:542 ; HOH:543 ; HOH:544 ; HOH:545
HOH:546 ; HOH:547 ; HOH:548 ; HOH:549 ; HOH:550 ; HOH:551 ; HOH:552 ; HOH:553 ; HOH:554 ; HOH:555
HOH:556 ; HOH:557 ; HOH:558 ; HOH:559 ; HOH:560 ; HOH:561 ; HOH:562 ; HOH:563 ; HOH:564 ; HOH:565
HOH:566 ; HOH:567 ; HOH:569 ; HOH:570 ; HOH:571 ; HOH:573 ; HOH:574 ; HOH:575 ; HOH:576 ; HOH:577
HOH:578 ; HOH:579 ; HOH:580 ; HOH:581 ; HOH:582 ; HOH:583 ; HOH:584 ; HOH:585 ; HOH:587 ; HOH:588
HOH:589 ; HOH:590 ; HOH:591 ; HOH:592 ; HOH:593 ; HOH:594 ; HOH:597 ; HOH:598 ; HOH:600 ; HOH:601
HOH:602 ; HOH:604 ; HOH:607 ; HOH:608 ; HOH:609 ; HOH:610 ; HOH:612 ; HOH:613 ; HOH:614 ; HOH:616
HOH:617 ; HOH:618 ; HOH:619 ; HOH:620 ; HOH:621 ; HOH:622 ; HOH:623 ; HOH:625 ; HOH:626 ; HOH:628
HOH:629 ; HOH:630 ; HOH:632 ; HOH:633 ; HOH:634 ; HOH:635 ; HOH:636 ; HOH:637 ; HOH:638 ; HOH:639
HOH:640 ; HOH:641 ; HOH:642 ; HOH:643 ; HOH:644 ; HOH:645 ; HOH:646 ; HOH:647 ; HOH:649 ; HOH:650
HOH:651 ; HOH:652 ; HOH:653 ; HOH:654 ; HOH:655 ; HOH:656 ; HOH:657 ; HOH:658 ; HOH:659 ; HOH:660
HOH:661 ; HOH:662 ; HOH:663 ; HOH:664 ; HOH:665 ; HOH:667 ; HOH:668
Link P::PO3:197::A OG1::THR:197::A GenericSingle
LeftTermination LYS:8
RightTermination PHE:350
End
Chain B
... very similar to chain A ...
End
Chain I
20
THR:1 ; THR:2 ; TYR:3 ; ALA:4 ; ASP:5 ; PHE:6 ; ILE:7 ; ALA:8 ; SER:9 ; GLY:10
ARG:11 ; THR:12 ; GLY:13 ; ARG:14 ; ARG:15 ; ASN:16 ; ALA:17 ; ILE:18 ; HIS:19 ; ASP:20
LeftTermination THR:1
RightTermination ASP:20
End
Chain J
... very similar to chain I ...
End
End
The file starts with the keyword PDBModel, followed by the title from the PDB file if one was found. After this come a series of blocks, enclosed between the keywords Chain and End, that specify the composition of the chains found in the PDB file. The file terminates with the word End.
The PDB file contains two, essentially identical, pairs of two chains — A/I and B/J — and so only one set is shown. Chain A is the catalytic subunit of PKA whereas chain I is the peptide inhibitor. The amino-acid sequences of both chains are listed and the N-terminal and C-terminal residues are explicitly identified with the LeftTermination and RightTermination keywords, respectively. In contrast to chain I, A contains residues other than amino acids. These are listed after the C-terminal residue, PHE:350, and comprise a phosphate (PO3:197), a 5'-adenyly-imido-triphosphate (ANP:400), two manganese ions (MN:401 and MN:402), a myristic acid (MYR:403) and 149 waters (HOH:500 to HOH:668).
None of the non-amino-acid residues in chain A have covalent bonds with other residues, except for PO3:197 which is linked to the amino acid THR:197. This is indicated by the Link statement which gives the atoms between which there is a bond (P::PO3:197::A and OG1::THR:197::A) as well as the type of link (GenericSingle). Links are determined from the CONECT and SSBOND records in the PDB file, so if these records are absent no links will be found. Links from CONECT records are given the generic name GenericSingle whereas those from SSBOND records are labelled DisulfideBridge. Only inter-residue links are output to the model file and not those between atoms of the same residue. Links between residues of the same chain are printed within the chain's statement block whereas inter-chain links are printed at the end of the file before the final terminating End keyword.
To finish this section, it is worth remarking that the file 1CDK.pdb contains only a single PDB model. Some PDB files, though, contain multiple models — most notably for files containing structures that have been resolved by NMR spectroscopy. In such cases, the desired model can be selected from the file by passing the modelNumber keyword argument to the PDBFile_ToPDBModel function. By default, the first model on the file is returned.
