-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathptm-extension.dic
1361 lines (1305 loc) · 56.9 KB
/
ptm-extension.dic
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# ----------------------------------------------------------------------------------------------------------------------------
#
# File: ptm-extension.dic
# Date: 26-May-2023 MGB
# Update: 26-May-2023
#
# Dictionary extensions for:
# - Extending the chemical components definition to backbone, N-terminal and C-terminal flags
# - Extending the chemical components definition to support the description of protein modifications
# - Extending the model definition to support annotation of protein modifications in the model
#
# PDBX_CHEM_COMP_PCM - Lists all the protein modifications that the chemical component can be used to describe
#
# PDBX_MODIFICATION_FEATURE - Lists all the protein modifications in the model
#
# ----------------------------------------------------------------------------------------------------------------------------
data_ptm-extension.dic
##################
# Meta Data #
##################
_pdbx_dictionary_component.datablock_id ptm-extension.dic
_pdbx_dictionary_component.dictionary_component_id ptm-extension.dic
_pdbx_dictionary_component.title "PDBx/mmCIF PTM extension"
_pdbx_dictionary_component.version 0.10
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
0.1 2023-05-26
;
Changes (mgb)
+ added new item type for UniProt PTM Accession IDs (PTM-XXXX)
+ added new item for PTM project to flag if the CCD can be used to
represent a protein modification
_chem_comp.pdbx_pcm
+ added new category for PTM project list all protein modifications in the entry
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
+ added new item for PTM project to flag if an entry contains protein modifications
_pdbx_entry_details.has_protein_modification
+ added new category for PTM project list all protein modifications in the entry
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
_pdbx_modification_feature.biological_function
_pdbx_modification_feature.biological_function_details
;
####################
# Item Types #
####################
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
uniprot_ptm_id char PTM-[0-9]{4} "UniProt PTM List Accession ID Pattern - PTM-XXXX"
###########################
# Parent/Child Links #
###########################
loop_
_pdbx_item_linked_group.category_id
_pdbx_item_linked_group.link_group_id
_pdbx_item_linked_group.label
_pdbx_item_linked_group.context
_pdbx_item_linked_group.condition_id
pdbx_chem_comp_pcm 1 pdbx_chem_comp_pcm:chem_comp:1 . .
pdbx_modification_feature 1 pdbx_modification_feature:atom_site:1 . .
pdbx_modification_feature 2 pdbx_modification_feature:atom_site:2 . .
loop_
_pdbx_item_linked_group_list.child_category_id
_pdbx_item_linked_group_list.link_group_id
_pdbx_item_linked_group_list.child_name
_pdbx_item_linked_group_list.parent_name
_pdbx_item_linked_group_list.parent_category_id
pdbx_chem_comp_pcm 1 "_pdbx_chem_comp_pcm.comp_id" "_chem_comp.id" chem_comp
pdbx_modification_feature 1 "_pdbx_modification_feature.label_comp_id" "_atom_site.label_comp_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.label_asym_id" "_atom_site.label_asym_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.label_seq_id" "_atom_site.label_seq_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.auth_comp_id" "_atom_site.auth_comp_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.auth_asym_id" "_atom_site.auth_asym_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.auth_seq_id" "_atom_site.auth_seq_id" atom_site
pdbx_modification_feature 1 "_pdbx_modification_feature.PDB_ins_code" "_atom_site.pdbx_PDB_ins_code" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_label_comp_id" "_atom_site.label_comp_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_label_asym_id" "_atom_site.label_asym_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_label_seq_id" "_atom_site.label_seq_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_auth_comp_id" "_atom_site.auth_comp_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_auth_asym_id" "_atom_site.auth_asym_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_auth_seq_id" "_atom_site.auth_seq_id" atom_site
pdbx_modification_feature 2 "_pdbx_modification_feature.modified_residue_PDB_ins_code" "_atom_site.pdbx_PDB_ins_code" atom_site
##################################################
# #
# PTM CCD Data Items #
# #
##################################################
##############################
# New item in _chem_comp #
##############################
#
save__chem_comp.pdbx_pcm
_item_description.description " A flag to indicate if the CCD can be used to represent a protein modification."
#
_item.name "_chem_comp.pdbx_pcm"
_item.category_id chem_comp
_item.mandatory_code no
#
_item_type.code code
_item_examples.case Y
#
loop_
_item_enumeration.value
_item_enumeration.detail
Y "Yes - Can be used to represent a protein modification"
N "No - Should never be used to represent a protein modification"
#
save_
#
####################################
# New items in _chem_comp_atom #
####################################
#
save__chem_comp_atom.pdbx_backbone_atom_flag
_item_description.description " A flag indicating the backbone atoms in polypeptide units."
#
_item.name "_chem_comp_atom.pdbx_backbone_atom_flag"
_item.category_id chem_comp_atom
_item.mandatory_code no
#
_item_type.code ucode
#
loop_
_item_enumeration.value
_item_enumeration.detail
Y "Yes - a part of the polypeptide backbone"
N "No - not part of the polypeptide backbone"
save_
#
save__chem_comp_atom.pdbx_n_terminal_atom_flag
_item_description.description " A flag indicating the N-terminal group atoms in polypeptide units."
#
_item.name "_chem_comp_atom.pdbx_n_terminal_atom_flag"
_item.category_id chem_comp_atom
_item.mandatory_code no
#
_item_type.code ucode
#
loop_
_item_enumeration.value
_item_enumeration.detail
Y "Yes - a part of the N-terminal group"
N "No - not part of the N-terminal group"
#
save_
#
save__chem_comp_atom.pdbx_c_terminal_atom_flag
_item_description.description " A flag indicating the C-terminal group atoms in polypeptide units."
#
_item.name "_chem_comp_atom.pdbx_c_terminal_atom_flag"
_item.category_id chem_comp_atom
_item.mandatory_code no
#
_item_type.code ucode
#
loop_
_item_enumeration.value
_item_enumeration.detail
Y "Yes - a part of the C-terminal group"
N "No - not part of the C-terminal group"
#
save_
#########################################
# New Category - pdbx_chem_comp_pcm #
#########################################
save_pdbx_chem_comp_pcm
_category.description
; Data items in the PDBX_CHEM_COMP_PCM category provide
information about the protein modifications that are described
by the chemical component.
;
_category.id pdbx_chem_comp_pcm
_category.mandatory_code no
#
_category_key.name "_pdbx_chem_comp_pcm.pcm_id"
#
loop_
_category_group.id
inclusive_group
chem_comp_dictionary_group
chem_comp_group
pdbx_group
#
loop_
_category_examples.detail
_category_examples.case
;
An example of the category for the phosphoserine (SEP) chemical component.
;
;
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 SEP SER Phosphorylation "Named protein modification" "Amino-acid side chain" "Any position" . . PTM-0253 ?
;
;
An example of the category for the Alpha-L-fucopyranose (FUC) chemical component.
;
;
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 FUC SER . Carbohydrate "Amino-acid side chain" "Any position" C1 OG ? ?
2 FUC THR . Carbohydrate "Amino-acid side chain" "Any position" C1 OG1 ? ?
;
#
save_
#
save__pdbx_chem_comp_pcm.pcm_id
_item_description.description " An ordinal index for this category."
#
_item.name "_pdbx_chem_comp_pcm.pcm_id"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code yes
#
_item_type.code int
_item_examples.case 1
#
save_
#
save__pdbx_chem_comp_pcm.comp_id
_item_description.description " Chemical component identifier for the CCD that contains the modification group."
#
_item.name "_pdbx_chem_comp_pcm.comp_id"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code yes
#
_item_linked.child_name "_pdbx_chem_comp_pcm.comp_id"
_item_linked.parent_name "_chem_comp.id"
#
_item_type.code ucode
_item_examples.case SEP
#
save_
#
save__pdbx_chem_comp_pcm.modified_residue_id
_item_description.description " Chemical component identifier for the amino acid residue that is being modified."
#
_item.name "_pdbx_chem_comp_pcm.modified_residue_id"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code uline
_item_examples.case SER
#
save_
#
save__pdbx_chem_comp_pcm.type
_item_description.description " The type of protein modification."
#
_item.name "_pdbx_chem_comp_pcm.type"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code line
_item_examples.case Phosphorylation
#
loop_
_item_enumeration.value
_item_enumeration.detail
"12-Hydroxyfarnesylation" .
"12-Oxomyristoylation" .
"12R-Hydroxymyristoylation" .
"14-Hydroxy-10,13-dioxo-7-heptadecenoic acid" .
"(3-Aminopropyl)(5'-adenosyl)phosphono amidation" .
"2-Aminoadipylation" .
"2-Aminoethylphosphorylation" .
"2-Cholinephosphorylation" .
"2-Hydroxyisobutyrylation" .
"2-Oxo-5,5-dimethylhexanoylation" .
"2-Oxobutanoic acid" .
"2,3-Dicarboxypropylation" .
"3-Oxoalanine" .
"3-Phenyllactic acid" .
"(3R)-3-Hydroxybutyrylation" .
"4-Phosphopantetheine" .
"ADP-ribosylation" .
"ADP-riboxanation" .
"AMPylation" .
"Acetamidation" .
"Acetamidomethylation" .
"Acetylation" .
"Allysine" .
"Amination" .
"Arachidoylation" .
"Archaeol" .
"Arsenylation" .
"Bacillithiolation" .
"Benzoylation" .
"Benzylation" .
"Beta-amino acid" .
"Beta-hydroxybutyrylation" .
"Beta-lysylation" .
"Beta-mercaptoethanol" .
"Biotinylation" .
"Bromination" .
"Butyrylation" .
"Carbamoylation" .
"Carboxyethylation" .
"Carboxylation" .
"Carboxymethylation" .
"cGMPylation" .
"Chlorination" .
"Cholesterylation" .
"Citrullination" .
"Crotonylation" .
"Cyanation" .
"D-amino acid" .
"Deamidation" .
"Decanoylation" .
"Decarboxylation" .
"Dehydroamino acid" .
"Dehydrocoelenterazination" .
"Dehydrogenation" .
"Dehydroxylation" .
"Deoxidation" .
"Deoxyhypusine" .
"Diacylglycerol" .
"Dihydroxyacetonation" .
"Diphosphorylation" .
"Diphthamide" .
"Dipyrromethane methylation" .
"Dopaminylation" .
"Ethylation" .
"Ethylsulfanylation" .
"Farnesylation" .
"Fluorination" .
"Formylation" .
"GMPylation" .
"Geranylgeranylation" .
"Glutarylation" .
"Glutathionylation" .
"Glycerophosphorylation" .
"Glycerylphosphorylethanolamination" .
"Heptanoylation" .
"Hexanoylation" .
"Histaminylation" .
"Hydrogenation" .
"Hydroperoxylation" .
"Hydroxylation" .
"Hypusine" .
"Iodination" .
"Lactoylation" .
"Laurylation" .
"Lipoylation" .
"Malonylation" .
"Methoxylation" .
"Methylamination" .
"Methylation" .
"Methylsulfanylation" .
"Methylsulfation" .
"Myristoylation" .
"N-pyruvic acid 2-iminylation" .
"Nitration" .
"Nitrosylation" .
"Noradrenylation" .
"Norleucine" .
"Octanoylation" .
"Oleoylation" .
"Ornithine" .
"Oxidation" .
"Palmitoleoylation" .
"Palmitoylation" .
"Pentadecanoylation" .
"Pentanoylation" .
"Phosphatidylethanolamine amidation" .
"Phosphoenolpyruvate" .
"Phosphorylation" .
"Propionylation" .
"Pyridoxal phosphate" .
"Pyrrolidone carboxylic acid" .
"Pyruvic acid" .
"Retinoylation" .
"Selanylation" .
"Selenocysteine" .
"Selenomethionine" .
"Serotonylation" .
"Stearoylation" .
"Stereoisomerisation" .
"Succinamide ring" .
"Succination" .
"Succinylation" .
"Sulfation" .
"Sulfhydration" .
"Sulfonation" .
"Tert-butylation" .
"Thyroxine" .
"Triiodothyronine" .
"UMPylation" .
#
save_
#
save__pdbx_chem_comp_pcm.category
_item_description.description " The category of protein modification."
#
_item.name "_pdbx_chem_comp_pcm.category"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code yes
#
_item_type.code line
_item_examples.case "Named protein modification"
#
loop_
_item_enumeration.value
_item_enumeration.detail
"ADP-Ribose" "ADP-ribose protein modifications"
"Biotin" "Biotin protein modifications"
"Carbohydrate" "Carbohydrate protein modifications"
"Chromophore/chromophore-like" "Chromophore or chromophore-like protein modifications"
"Covalent chemical modification" "A diverse range of chemical compounds that form covalent bonds with amino acids. Not covered by any of the other modification categories"
"Crosslinker" "STILL BEING DEFINED"
"Disulfide" "Disulfide bridge protein modifications"
"Flavin" "Flavin protein modifications"
"Heme/heme-like" "Heme or heme-like protein modifications "
"Lipid/lipid-like" "Lipid or lipid-like protein modifications"
"Named protein modification" "All protein modifications that are well defined into known types, have limited diversity, and are not explicitly covered by any other category. It includes PTMs, PCMs, rare amino acids and unnatural amino acids"
"Non-standard linkage" "Non-standard covalent chemical linkages directly between two polypeptide residues"
"Non-standard residue" "A diverse range of non-standard polypeptide residues that are not considered to be 'Named protein modifications'. These cannot be practically split into two CCDs, which describe the standard polypeptide residue and the modification group, and are not covered by any of the other modification categories"
"Nucleotide monophosphate" "Nucleotide monophosphate protein modifications"
"Terminal acetylation" "Terminal acetylation protein modification"
"Terminal amidation" "Terminal amidation protein modification"
#
save_
#
save__pdbx_chem_comp_pcm.position
_item_description.description " The position of the modification on the amino acid."
#
_item.name "_pdbx_chem_comp_pcm.position"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code yes
#
_item_type.code line
_item_examples.case "Amino acid side chain"
#
loop_
_item_enumeration.value
_item_enumeration.detail
"Amino-acid side chain" "Protein modification occurs on the amino acid side chain"
"Amino-acid backbone" "Protein modification occurs on the amino acid backbone"
"Amino-acid side chain and backbone" "Protein modification occurs on both the amino acid side chain and backbone"
#
save_
#
save__pdbx_chem_comp_pcm.polypeptide_position
_item_description.description " The position of the modification on the polypeptide."
#
_item.name "_pdbx_chem_comp_pcm.polypeptide_position"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code yes
#
_item_type.code line
_item_examples.case "Any position"
#
loop_
_item_enumeration.value
_item_enumeration.detail
"C-terminal" "Protein modification can only occur on C-terminus"
"N-terminal" "Protein modification can only occur on N-terminus"
"Any position" "Protein modification can occur in any position of the polypeptide sequence"
#
save_
#
save__pdbx_chem_comp_pcm.comp_id_linking_atom
_item_description.description
; The atom on the modification group that covalently links the
modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
;
#
_item.name "_pdbx_chem_comp_pcm.comp_id_linking_atom"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code atcode
_item_examples.case C1
#
save_
#
save__pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_item_description.description
; The atom on the polypeptide residue group that covalently links
the modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
;
#
_item.name "_pdbx_chem_comp_pcm.modified_residue_id_linking_atom"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code atcode
_item_examples.case OG
#
save_
#
save__pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_item_description.description " The UniProt PTM accession code that is an exact match for the protein modification."
#
_item.name "_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code uniprot_ptm_id
_item_examples.case PTM-0253
#
save_
#
save__pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
_item_description.description " The UniProt PTM accession code that describes the group of PTMs of which this protein modification is a member."
#
_item.name "_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code uniprot_ptm_id
_item_examples.case PTM-0252
#
save_
#############################################
# Internal items for pdbx_chem_comp_pcm #
#############################################
#
save__pdbx_chem_comp_pcm.first_instance_model_db_code
_item_description.description " The PDB Entry ID for the first model that contains the protein modification."
#
_item.name "_pdbx_chem_comp_pcm.first_instance_model_db_code"
_item.category_id pdbx_chem_comp_pcm
_item.mandatory_code no
#
_item_type.code line
_item_examples.case 4PEP
#
_pdbx_item_context.type WWPDB_LOCAL
_pdbx_item_context.item_name "_pdbx_chem_comp_pcm.first_instance_model_db_code"
#
save_
##################################################
# #
# PTM mmCIF Data Items #
# #
##################################################
#######################################
# New item in _pdbx_entry_details #
#######################################
#
save__pdbx_entry_details.has_protein_modification
_item_description.description " A flag to indicate if the model contains any protein modifications."
#
_item.name "_pdbx_entry_details.has_protein_modification"
_item.category_id pdbx_entry_details
_item.mandatory_code no
#
_item_type.code code
_item_examples.case Y
#
loop_
_item_enumeration.value
_item_enumeration.detail
Y "Protein modification present"
#
save_
#
################################################
# New Category - pdbx_modification_feature #
################################################
save_pdbx_modification_feature
_category.description
; Data items in the PDBX_MODIFICATION_FEATURE category provides
information about all the protein modifications that have been
modeled in the entry.
;
_category.id pdbx_modification_feature
_category.mandatory_code no
#
_category_key.name "_pdbx_modification_feature.ordinal"
#
loop_
_category_group.id
inclusive_group
struct_group
#
loop_
_category_examples.detail
_category_examples.case
;
An example of the category in an entry that contains a disulfide bridge and
two phosphoserine modifications.
;
;
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
_pdbx_modification_feature.biological_function
_pdbx_modification_feature.biological_function_details
1 CYS B 46 CYS A 46 CYS B 46 ? CYS A 46 ? SG SG . . . . Disulfide ? ?
2 SEP A 65 . . . SEP A 65 ? . . . . . . SER 1 SEP Phosphorylation 'Named protein modification' ? ?
3 SEP B 65 . . . SEP B 65 ? . . . . . . SER 1 SEP Phosphorylation 'Named protein modification' ? ?
;
;
An example of the category in an entry that contains a two cysteine
hydroxylation modification sites and two palmitoylation modification sites.
;
;
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
_pdbx_modification_feature.biological_function
_pdbx_modification_feature.biological_function_details
1 CSO C 32 . . . CSO C 32 ? . . . . . . CYS 1 CSO Hydroxylation 'Named protein modification' ? ?
2 CSO D 32 . . . CSO D 32 ? . . . . . . CYS 1 CSO Hydroxylation 'Named protein modification' ? ?
3 PLM E . CYS A 82 PLM A 1068 ? CYS A 68 ? C1 SG CYS 6 PLM Palmitoylation 'Lipid/lipid-like' ? ?
4 PLM F . CYS B 82 PLM B 1068 ? CYS B 68 ? C1 SG CYS 6 PLM Palmitoylation 'Lipid/lipid-like' ? ?
;
#
save_
#
save__pdbx_modification_feature.ordinal
_item_description.description " An ordinal index for this category."
#
_item.name "_pdbx_modification_feature.ordinal"
_item.category_id pdbx_modification_feature
_item.mandatory_code yes
#
_item_type.code int
_item_examples.case 1
#
save_
#
save__pdbx_modification_feature.label_comp_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.label_comp_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code yes
#
_item_linked.child_name "_pdbx_modification_feature.label_comp_id"
_item_linked.parent_name "_atom_site.label_comp_id"
#
_item_type.code ucode
#
loop_
_item_examples.case
"SEP"
"PLM"
#
save_
#
save__pdbx_modification_feature.label_asym_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.label_asym_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code yes
#
_item_linked.child_name "_pdbx_modification_feature.label_asym_id"
_item_linked.parent_name "_atom_site.label_asym_id"
#
_item_type.code code
_item_examples.case E
#
save_
#
save__pdbx_modification_feature.label_seq_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.label_seq_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.label_seq_id"
_item_linked.parent_name "_atom_site.label_seq_id"
#
_item_type.code int
_item_examples.case 65
#
save_
#
save__pdbx_modification_feature.modified_residue_label_comp_id
_item_description.description
; A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.modified_residue_label_comp_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.modified_residue_label_comp_id"
_item_linked.parent_name "_atom_site.label_comp_id"
#
_item_type.code ucode
_item_examples.case CYS
#
save_
#
save__pdbx_modification_feature.modified_residue_label_asym_id
_item_description.description
; A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.modified_residue_label_asym_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.modified_residue_label_asym_id"
_item_linked.parent_name "_atom_site.label_asym_id"
#
_item_type.code code
_item_examples.case A
#
save_
#
save__pdbx_modification_feature.modified_residue_label_seq_id
_item_description.description
; A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.modified_residue_label_seq_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.modified_residue_label_seq_id"
_item_linked.parent_name "_atom_site.label_seq_id"
#
_item_type.code int
_item_examples.case 82
#
save_
#
save__pdbx_modification_feature.auth_comp_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.auth_comp_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.auth_comp_id"
_item_linked.parent_name "_atom_site.auth_comp_id"
#
_item_type.code code
_item_examples.case PLM
#
save_
#
save__pdbx_modification_feature.auth_asym_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.auth_asym_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.auth_asym_id"
_item_linked.parent_name "_atom_site.auth_asym_id"
#
_item_type.code code
_item_examples.case A
#
save_
#
save__pdbx_modification_feature.auth_seq_id
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.auth_seq_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.auth_seq_id"
_item_linked.parent_name "_atom_site.auth_seq_id"
#
_item_type.code code
_item_examples.case 65
#
save_
#
save__pdbx_modification_feature.PDB_ins_code
_item_description.description
; A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.PDB_ins_code"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.PDB_ins_code"
_item_linked.parent_name "_atom_site.pdbx_PDB_ins_code"
#
_item_type.code code
_item_examples.case 1
#
save_
#
save__pdbx_modification_feature.modified_residue_auth_comp_id
_item_description.description
; A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
#
_item.name "_pdbx_modification_feature.modified_residue_auth_comp_id"
_item.category_id pdbx_modification_feature
_item.mandatory_code no
#
_item_linked.child_name "_pdbx_modification_feature.modified_residue_auth_comp_id"
_item_linked.parent_name "_atom_site.auth_comp_id"
#
_item_type.code code
_item_examples.case CYS
#
save_
#