Basic Information
This Gist is a personal note that recording those issues encountered during my use cases.
API References
PDBe REST API
- https://www.ebi.ac.uk/pdbe/api/doc/pdb.html
- https://www.ebi.ac.uk/pdbe/api/doc/pisa.html
- https://www.ebi.ac.uk/pdbe/api/doc/sifts.html
PDBe Graph API
Neo4j Graph DataBase
PDBe CoordinateServer API
PDBe ModelServer API
Chain Identifier Related
mmCIF’s Internal ID Synonym- Named:
'asym chain id' struct_asym_id(implement by PDBe REST API)label_asym_id(implement by PDBe ModelServer API)asymId(implement by PDBe CoordinateServer API)
- Named:
PDBFormat, ‘traditional’ ID Synonym- Named:
'auth chain id' chain_id(implement by PDBe REST API)auth_asym_id(implement by PDBe ModelServer API)authAsymId(implement by PDBe CoordinateServer API)
- Named:
Related Issues
- https://github.com/biojava/biojava/issues/469: Add better support for asym chain ids as well as auth ids
- https://github.com/biojava/biojava/pull/479: Refactoring of structure data model
Biological Assemblies Related
Issue: struct_asym_id in assembly/ in_chains generate new struct_asym_id
Example:
| pdb_id | entity_id | in_struct_asyms | molecule_type |
| 2o2q | 1 | ["A","B","C","D"] | polypeptide(L) |
| 2o2q | 2 | ["E","JA","Q","Z"] | bound |
| 2o2q | 3 | ["AA","BA","CA","DA","EA","F","FA","G","GA","H","I","J","K","KA","L","LA","M","MA","N","NA","OA","PA","R","S","T","U","V","W"] | bound |
| 2o2q | 4 | ["HA","O","QA","X"] | bound |
| 2o2q | 5 | ["IA","P","RA","Y"] | bound |
| 2o2q | 6 | ["SA","TA","UA","VA"] | water |
provided by https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/2o2q
| pdb_id | assembly_id | entity_id | in_chains |
| 2o2q | 1 | 1 | ["A","B","C","D"] |
| 2o2q | 1 | 2 | ["E","JA","Q","Z"] |
| 2o2q | 1 | 3 | ["AA","BA","CA","DA","EA","F","FA","G","GA","H","I","J","K","KA","L","LA","M","MA","N","NA","OA","PA","R","S","T","U","V","W"] |
| 2o2q | 1 | 4 | ["HA","O","QA","X"] |
| 2o2q | 1 | 5 | ["IA","P","RA","Y"] |
| 2o2q | 1 | 6 | ["SA","TA","UA","VA"] |
| 2o2q | 3 | 1 | ["A","AA","B","BA","C","CB","D","DB"] |
| 2o2q | 3 | 2 | ["E","EA","JB","JC","Q","QA","Z","ZA"] |
| 2o2q | 3 | 3 | ["AB","AC","BB","BC","CA","CC","DA","DC","EB","EC","F","FA","FB","FC","G","GA","GB","GC","H","HA","I","IA","J","JA","K","KA","KB","KC","L","LA","LB","LC","M","MA","MB","MC","N","NA","NB","NC","OB","OC","PB","PC","R","RA","S","SB","T","TB","U","UA","V","VA","W","WA"] |
| 2o2q | 3 | 4 | ["HB","HC","O","OA","QB","QC","X","XA"] |
| 2o2q | 3 | 5 | ["IB","IC","P","PA","RB","RC","Y","YA"] |
| 2o2q | 3 | 6 | ["SA","SC","TA","TC","UB","UC","VB","VC"] |
| 2o2q | 2 | 1 | ["A","AB","B","BB","C","CB","D","DB"] |
| 2o2q | 2 | 2 | ["E","EB","JA","JC","Q","QB","Z","ZA"] |
| 2o2q | 2 | 3 | ["AA","AC","BA","BC","CA","CC","DA","DC","EA","EC","F","FA","FB","FC","G","GA","GB","GC","H","HB","I","IB","J","JB","K","KA","KB","KC","L","LA","LB","LC","M","MA","MB","MC","N","NA","NB","NC","OA","OC","PA","PC","R","RB","S","SB","T","TB","U","UB","V","VB","W","WA"] |
| 2o2q | 2 | 4 | ["HA","HC","O","OB","QA","QC","X","XA"] |
| 2o2q | 2 | 5 | ["IA","IC","P","PB","RA","RC","Y","YA"] |
| 2o2q | 2 | 6 | ["SA","SC","TA","TC","UA","UC","VA","VC"] |
provided by https://www.ebi.ac.uk/pdbe/api/pdb/entry/assembly/2o2q
The in_chains column contains a new version of struct_asym_id for that particular assemble and entity. The rule seems to be like this: In a specified assemble, for those original chains, keep their original struct_asym_id; for those replicated chains, generate new struct_asym_id that continues the original chain’s struct_asym_id while not in collision with existing struct_asym_id in that assemble (i.e. assembly3’s <entity3’s PB PC><entity5’s PA>, assembly2’s <entity3’s PA PC><entity5’s PB>).
And I found that the ID of chain provided by PDBe PISA API (i.e. https://www.ebi.ac.uk/pdbe/api/pisa/interfacelist/2o2q/3) are corresponding to the above ID (at least in my usage cases):
| structure_1.range | structure_2.range | interface_id |
| D | C | 1 |
| DB | CB | 2 |
| [GOL]YA:2 | BA | 20 |
| [GOL]PA:1 | AA | 22 |
Since I can get all the struct_asym_id in the asymmetric unit and their replication result from mmCIF’s _pdbx_struct_assembly_gen and _pdbx_struct_oper_list and I can infer their model_id and ranking:
| assembly_id | struct_asym_id | model_id | asym_id_rank | oper_expression | symmetry_operation |
| 2 | P | 1 | 1 | ["1"] | ["x,y,z"] |
| 2 | P | 2 | 2 | ["2"] | ["-x+1,y,-z+1"] |
| 2 | PA | 1 | 1 | ["1"] | ["x,y,z"] |
| 2 | PA | 2 | 2 | ["2"] | ["-x+1,y,-z+1"] |
| 3 | P | 1 | 1 | ["1"] | ["x,y,z"] |
| 3 | P | 2 | 2 | ["3"] | ["-x+1,y,-z"] |
| 3 | PA | 3 | 1 | ["4"] | ["x,y,z-1"] |
| 3 | PA | 4 | 2 | ["2"] | ["-x+1,y,-z+1"] |
I would like to apply the automatic rule to generate corresponding new struct_asym_id for a specified assemble and map them with the interfacelist provided by PISA API.
The issue is, what is the automatic rule?
Related Issues
- https://github.com/biojava/biojava/issues/220: Better support for symmetry in the Structure model
- https://github.com/biojava/biojava/issues/801: Biological assembly expansion: chain ids should contain both operator ids in binary expression case
- https://github.com/biojava/biojava/pull/802: Assembly chain ids for cases with composed operators in assembly expansion
Carbohydrate Related
During my implementation of the REST calls related to PISA service, I found some ‘outdated’ information caused by the recent Carbohydrate Remediation Project. For instance, the chain identifiers of those carbohydrate polymers have now been regenerated in the current wwPDB archive file and also affect some other chain instance’s id.
Examples:
- 2wmg: NAGs, FUCs, GALs used to have their own struct_asym_id but now are aggregated into one single chain instance
- 1wdq: MAL -> GLC
- 2aw3: other chain instance’s struct_asym_id are also re-generated
I would like to know whether the PISA dataset would ‘update’ to keep pace with the Carbohydrate Remediation Project or not.
Externel Links
Issue: Outdated PISA dataset (e.g 2wmg)?
| entity_id | in_chains | in_struct_asyms | length | molecule_name | molecule_type | number_of_copies | pdb_id |
| 1 | ["A"] | ["A"] | 581 | ["F5/8 type C domain-containing protein"] | polypeptide(L) | 1 | 2wmg |
| 2 | ["B"] | ["B"] | ["alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose"] | carbohydrate polymer | 4 | 2wmg | |
| 3 | ["A"] | ["C"] | ["water"] | water | 334 | 2wmg |
provided by https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/2o2q
| structure_1.range | structure_2.range | css | delta_g_interface | structure_2.symmetry_operator |
| A | A | 0 | -0.372 | x-1/2,-y+1/2,-z+1 |
| A | A | 0 | -0.906674 | -x+1,y-1/2,-z+1/2 |
| A | A | 0 | -0.105273 | x-1,y,z |
| [NAG]D:1592 | A | 0 | 2.37148 | x,y,z |
| [FUC]B:1590 | A | 0 | 1.67611 | x,y,z |
| [GAL]C:1591 | A | 0 | 2.43961 | x,y,z |
| [FUC]E:1593 | A | 0 | 1.46851 | x,y,z |
| A | A | 0 | -0.656549 | -x,y-1/2,-z+1/2 |
| [NAG]D:1592 | [GAL]C:1591 | 0 | 1.25173 | x,y,z |
| [NAG]D:1592 | [FUC]E:1593 | 0 | 2.05322 | x,y,z |
| [GAL]C:1591 | [FUC]E:1593 | 0 | 1.44298 | x,y,z |
| [GAL]C:1591 | [FUC]B:1590 | 0 | 1.95678 | x,y,z |
| [FUC]E:1593 | [FUC]B:1590 | 0 | 1.98391 | x,y,z |
| A | A | 0 | -0.497071 | -x+1/2,-y+1,z-1/2 |
| [NAG]D:1592 | [FUC]B:1590 | 0 | 0.398597 | x,y,z |
provided by https://www.ebi.ac.uk/pdbe/api/pisa/interfacelist/2o2q/0
Look into wwPDB Archive
HETATM 4499 C C1 . FUC B 2 . ? 21.448 30.534 21.369 1.00 26.82 ? 1590 FUC A C1 1
HETATM 4500 C C2 . FUC B 2 . ? 20.079 29.853 21.519 1.00 26.87 ? 1590 FUC A C2 1
HETATM 4501 C C3 . FUC B 2 . ? 19.240 30.667 22.520 1.00 26.92 ? 1590 FUC A C3 1
HETATM 4502 C C4 . FUC B 2 . ? 19.073 32.098 21.990 1.00 26.06 ? 1590 FUC A C4 1
HETATM 4503 C C5 . FUC B 2 . ? 20.468 32.708 21.723 1.00 27.34 ? 1590 FUC A C5 1
HETATM 4504 C C6 . FUC B 2 . ? 20.412 34.110 21.105 1.00 27.22 ? 1590 FUC A C6 1
HETATM 4505 O O2 . FUC B 2 . ? 20.211 28.500 21.918 1.00 27.52 ? 1590 FUC A O2 1
HETATM 4506 O O3 . FUC B 2 . ? 17.984 30.074 22.824 1.00 27.23 ? 1590 FUC A O3 1
HETATM 4507 O O4 . FUC B 2 . ? 18.250 32.100 20.836 1.00 22.93 ? 1590 FUC A O4 1
HETATM 4508 O O5 . FUC B 2 . ? 21.275 31.860 20.900 1.00 27.65 ? 1590 FUC A O5 1
HETATM 4509 C C1 . GAL C 3 . ? 23.982 31.388 23.800 1.00 28.73 ? 1591 GAL A C1 1
HETATM 4510 C C2 . GAL C 3 . ? 23.540 30.520 22.595 1.00 27.78 ? 1591 GAL A C2 1
HETATM 4511 C C3 . GAL C 3 . ? 24.078 29.067 22.652 1.00 26.81 ? 1591 GAL A C3 1
HETATM 4512 C C4 . GAL C 3 . ? 25.532 29.029 23.115 1.00 27.03 ? 1591 GAL A C4 1
HETATM 4513 C C5 . GAL C 3 . ? 25.614 29.712 24.483 1.00 27.02 ? 1591 GAL A C5 1
HETATM 4514 C C6 . GAL C 3 . ? 27.020 29.735 25.059 1.00 26.52 ? 1591 GAL A C6 1
HETATM 4515 O O2 . GAL C 3 . ? 22.125 30.492 22.645 1.00 28.02 ? 1591 GAL A O2 1
HETATM 4516 O O3 . GAL C 3 . ? 23.954 28.363 21.425 1.00 24.40 ? 1591 GAL A O3 1
HETATM 4517 O O4 . GAL C 3 . ? 26.389 29.623 22.145 1.00 26.50 ? 1591 GAL A O4 1
HETATM 4518 O O5 . GAL C 3 . ? 25.240 31.061 24.376 1.00 28.14 ? 1591 GAL A O5 1
HETATM 4519 O O6 . GAL C 3 . ? 26.910 30.176 26.391 1.00 26.25 ? 1591 GAL A O6 1
HETATM 4520 C C1 . NAG D 4 . ? 26.561 36.013 23.263 1.00 35.36 ? 1592 NAG A C1 1
HETATM 4521 C C2 . NAG D 4 . ? 26.575 35.095 22.025 1.00 36.05 ? 1592 NAG A C2 1
HETATM 4522 C C3 . NAG D 4 . ? 25.434 34.037 22.061 1.00 35.34 ? 1592 NAG A C3 1
HETATM 4523 C C4 . NAG D 4 . ? 25.202 33.442 23.473 1.00 33.52 ? 1592 NAG A C4 1
HETATM 4524 C C5 . NAG D 4 . ? 25.377 34.458 24.623 1.00 34.35 ? 1592 NAG A C5 1
HETATM 4525 C C6 . NAG D 4 . ? 25.450 33.779 25.994 1.00 34.59 ? 1592 NAG A C6 1
HETATM 4526 C C7 . NAG D 4 . ? 27.588 36.194 20.056 1.00 37.78 ? 1592 NAG A C7 1
HETATM 4527 C C8 . NAG D 4 . ? 27.375 37.110 18.885 1.00 37.94 ? 1592 NAG A C8 1
HETATM 4528 N N2 . NAG D 4 . ? 26.519 35.920 20.818 1.00 36.64 ? 1592 NAG A N2 1
HETATM 4529 O O1 . NAG D 4 . ? 27.692 36.861 23.312 1.00 35.52 ? 1592 NAG A O1 1
HETATM 4530 O O3 . NAG D 4 . ? 25.589 32.903 21.193 1.00 35.46 ? 1592 NAG A O3 1
HETATM 4531 O O4 . NAG D 4 . ? 23.913 32.818 23.523 1.00 31.47 ? 1592 NAG A O4 1
HETATM 4532 O O5 . NAG D 4 . ? 26.546 35.245 24.449 1.00 35.47 ? 1592 NAG A O5 1
HETATM 4533 O O6 . NAG D 4 . ? 25.836 34.672 27.021 1.00 34.34 ? 1592 NAG A O6 1
HETATM 4534 O O7 . NAG D 4 . ? 28.715 35.736 20.261 1.00 38.61 ? 1592 NAG A O7 1
HETATM 4535 C C1 . FUC E 2 . ? 25.747 33.116 19.759 1.00 35.63 ? 1593 FUC A C1 1
HETATM 4536 C C2 . FUC E 2 . ? 25.953 31.766 19.050 1.00 35.47 ? 1593 FUC A C2 1
HETATM 4537 C C3 . FUC E 2 . ? 24.620 31.032 18.831 1.00 35.29 ? 1593 FUC A C3 1
HETATM 4538 C C4 . FUC E 2 . ? 23.605 31.935 18.138 1.00 34.97 ? 1593 FUC A C4 1
HETATM 4539 C C5 . FUC E 2 . ? 23.486 33.285 18.870 1.00 35.29 ? 1593 FUC A C5 1
HETATM 4540 C C6 . FUC E 2 . ? 22.572 34.252 18.123 1.00 33.61 ? 1593 FUC A C6 1
HETATM 4541 O O2 . FUC E 2 . ? 26.834 30.951 19.799 1.00 34.72 ? 1593 FUC A O2 1
HETATM 4542 O O3 . FUC E 2 . ? 24.793 29.854 18.066 1.00 34.23 ? 1593 FUC A O3 1
HETATM 4543 O O4 . FUC E 2 . ? 23.980 32.080 16.780 1.00 35.78 ? 1593 FUC A O4 1
HETATM 4544 O O5 . FUC E 2 . ? 24.751 33.904 19.097 1.00 35.04 ? 1593 FUC A O5 1
HETATM 4499 C C1 . NAG B 2 . ? 26.561 36.013 23.263 1.00 35.36 ? 1 NAG B C1 1 1
HETATM 4500 C C2 . NAG B 2 . ? 26.575 35.095 22.025 1.00 36.05 ? 1 NAG B C2 1 1
HETATM 4501 C C3 . NAG B 2 . ? 25.434 34.037 22.061 1.00 35.34 ? 1 NAG B C3 1 1
HETATM 4502 C C4 . NAG B 2 . ? 25.202 33.442 23.473 1.00 33.52 ? 1 NAG B C4 1 1
HETATM 4503 C C5 . NAG B 2 . ? 25.377 34.458 24.623 1.00 34.35 ? 1 NAG B C5 1 1
HETATM 4504 C C6 . NAG B 2 . ? 25.450 33.779 25.994 1.00 34.59 ? 1 NAG B C6 1 1
HETATM 4505 C C7 . NAG B 2 . ? 27.588 36.194 20.056 1.00 37.78 ? 1 NAG B C7 1 1
HETATM 4506 C C8 . NAG B 2 . ? 27.375 37.110 18.885 1.00 37.94 ? 1 NAG B C8 1 1
HETATM 4507 N N2 . NAG B 2 . ? 26.519 35.920 20.818 1.00 36.64 ? 1 NAG B N2 1 1
HETATM 4508 O O1 . NAG B 2 . ? 27.692 36.861 23.312 1.00 35.52 ? 1 NAG B O1 1 1
HETATM 4509 O O3 . NAG B 2 . ? 25.589 32.903 21.193 1.00 35.46 ? 1 NAG B O3 1 1
HETATM 4510 O O4 . NAG B 2 . ? 23.913 32.818 23.523 1.00 31.47 ? 1 NAG B O4 1 1
HETATM 4511 O O5 . NAG B 2 . ? 26.546 35.245 24.449 1.00 35.47 ? 1 NAG B O5 1 1
HETATM 4512 O O6 . NAG B 2 . ? 25.836 34.672 27.021 1.00 34.34 ? 1 NAG B O6 1 1
HETATM 4513 O O7 . NAG B 2 . ? 28.715 35.736 20.261 1.00 38.61 ? 1 NAG B O7 1 1
HETATM 4514 C C1 . GAL B 2 . ? 23.982 31.388 23.800 1.00 28.73 ? 2 GAL B C1 1 2
HETATM 4515 C C2 . GAL B 2 . ? 23.540 30.520 22.595 1.00 27.78 ? 2 GAL B C2 1 2
HETATM 4516 C C3 . GAL B 2 . ? 24.078 29.067 22.652 1.00 26.81 ? 2 GAL B C3 1 2
HETATM 4517 C C4 . GAL B 2 . ? 25.532 29.029 23.115 1.00 27.03 ? 2 GAL B C4 1 2
HETATM 4518 C C5 . GAL B 2 . ? 25.614 29.712 24.483 1.00 27.02 ? 2 GAL B C5 1 2
HETATM 4519 C C6 . GAL B 2 . ? 27.020 29.735 25.059 1.00 26.52 ? 2 GAL B C6 1 2
HETATM 4520 O O2 . GAL B 2 . ? 22.125 30.492 22.645 1.00 28.02 ? 2 GAL B O2 1 2
HETATM 4521 O O3 . GAL B 2 . ? 23.954 28.363 21.425 1.00 24.40 ? 2 GAL B O3 1 2
HETATM 4522 O O4 . GAL B 2 . ? 26.389 29.623 22.145 1.00 26.50 ? 2 GAL B O4 1 2
HETATM 4523 O O5 . GAL B 2 . ? 25.240 31.061 24.376 1.00 28.14 ? 2 GAL B O5 1 2
HETATM 4524 O O6 . GAL B 2 . ? 26.910 30.176 26.391 1.00 26.25 ? 2 GAL B O6 1 2
HETATM 4525 C C1 . FUC B 2 . ? 21.448 30.534 21.369 1.00 26.82 ? 3 FUC B C1 1 3
HETATM 4526 C C2 . FUC B 2 . ? 20.079 29.853 21.519 1.00 26.87 ? 3 FUC B C2 1 3
HETATM 4527 C C3 . FUC B 2 . ? 19.240 30.667 22.520 1.00 26.92 ? 3 FUC B C3 1 3
HETATM 4528 C C4 . FUC B 2 . ? 19.073 32.098 21.990 1.00 26.06 ? 3 FUC B C4 1 3
HETATM 4529 C C5 . FUC B 2 . ? 20.468 32.708 21.723 1.00 27.34 ? 3 FUC B C5 1 3
HETATM 4530 C C6 . FUC B 2 . ? 20.412 34.110 21.105 1.00 27.22 ? 3 FUC B C6 1 3
HETATM 4531 O O2 . FUC B 2 . ? 20.211 28.500 21.918 1.00 27.52 ? 3 FUC B O2 1 3
HETATM 4532 O O3 . FUC B 2 . ? 17.984 30.074 22.824 1.00 27.23 ? 3 FUC B O3 1 3
HETATM 4533 O O4 . FUC B 2 . ? 18.250 32.100 20.836 1.00 22.93 ? 3 FUC B O4 1 3
HETATM 4534 O O5 . FUC B 2 . ? 21.275 31.860 20.900 1.00 27.65 ? 3 FUC B O5 1 3
HETATM 4535 C C1 . FUC B 2 . ? 25.747 33.116 19.759 1.00 35.63 ? 4 FUC B C1 1 4
HETATM 4536 C C2 . FUC B 2 . ? 25.953 31.766 19.050 1.00 35.47 ? 4 FUC B C2 1 4
HETATM 4537 C C3 . FUC B 2 . ? 24.620 31.032 18.831 1.00 35.29 ? 4 FUC B C3 1 4
HETATM 4538 C C4 . FUC B 2 . ? 23.605 31.935 18.138 1.00 34.97 ? 4 FUC B C4 1 4
HETATM 4539 C C5 . FUC B 2 . ? 23.486 33.285 18.870 1.00 35.29 ? 4 FUC B C5 1 4
HETATM 4540 C C6 . FUC B 2 . ? 22.572 34.252 18.123 1.00 33.61 ? 4 FUC B C6 1 4
HETATM 4541 O O2 . FUC B 2 . ? 26.834 30.951 19.799 1.00 34.72 ? 4 FUC B O2 1 4
HETATM 4542 O O3 . FUC B 2 . ? 24.793 29.854 18.066 1.00 34.23 ? 4 FUC B O3 1 4
HETATM 4543 O O4 . FUC B 2 . ? 23.980 32.080 16.780 1.00 35.78 ? 4 FUC B O4 1 4
HETATM 4544 O O5 . FUC B 2 . ? 24.751 33.904 19.097 1.00 35.04 ? 4 FUC B O5 1 4
Issue: Outdated PISA dataset (e.g 1wdq)?
| entity_id | gene_name | in_chains | in_struct_asyms | length | molecule_name | molecule_type | number_of_copies | pdb_id |
| 1 | ["BMY1"] | ["A"] | ["A"] | 495 | ["Beta-amylase"] | polypeptide(L) | 1 | 1wdq |
| 2 | ["B","C"] | ["B","C"] | ["alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose"] | carbohydrate polymer | 4 | 1wdq | ||
| 3 | ["A"] | ["D","E","F","G","H"] | ["SULFATE ION"] | bound | 5 | 1wdq | ||
| 4 | ["A"] | ["I"] | ["water"] | water | 810 | 1wdq |
provided by https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1wdq
| structure_1.range | structure_2.range | css | delta_g_interface | structure_2.symmetry_operator |
| A | A | 0 | -3.79762 | -x+1,-x+y,-z+1/3 |
| A | A | 0 | 3.33369 | y,x,-z |
| A | A | 0 | -1.49174 | -y+1,x-y+1,z+1/3 |
| [MAL]C:498 | A | 0.00698 | -0.294266 | x,y,z |
| [MAL]B:496 | A | 0.005702 | 0.047561 | x,y,z |
| A | A | 0 | -1.21817 | -x,-x+y,-z+1/3 |
| [SO4]D:2000 | A | 0.018727 | -9.73464 | x,y,z |
| [SO4]E:2001 | A | 0.022233 | -11.8895 | x,y,z |
| [SO4]F:2002 | A | 0.015819 | -8.83509 | x,y,z |
| [SO4]G:2003 | A | 0.016383 | -8.73819 | x,y,z |
| A | [SO4]H:2004 | 0.012637 | -7.32349 | -y+1,x-y+1,z+1/3 |
| [MAL]C:498 | [MAL]B:496 | 0.00027 | -0.165906 | x,y,z |
| [SO4]E:2001 | A | 0 | -4.81706 | -y+1,x-y+1,z+1/3 |
| [SO4]H:2004 | A | 0 | -3.47703 | x,y,z |
| A | [SO4]H:2004 | 0 | -5.19629 | -x+1,-x+y,-z+1/3 |
| A | [SO4]D:2000 | 0 | -3.3604 | -x+1,-x+y,-z+1/3 |
| [SO4]G:2003 | A | 0 | -2.768 | -x,-x+y,-z+1/3 |
| A | A | 0 | -0.079932 | x-y,-y+1,-z+2/3 |
| A | [SO4]E:2001 | 0 | -0.489989 | -x+1,-x+y,-z+1/3 |
| [SO4]E:2001 | [SO4]D:2000 | 0.001249 | -0.767584 | x,y,z |
provided by https://www.ebi.ac.uk/pdbe/api/pisa/interfacelist/1wdq/0
Look into wwPDB Archive
http://ftp-versioned.wwpdb.org/pdb_versioned/data/entries/wd/pdb_00001wdq/pdb_00001wdq_xyz_v1-2.cif.gz:
HETATM 3960 C C1 . MAL B 2 . ? 0.923 28.692 21.983 1.00 15.32 ? 496 MAL A C1 1
HETATM 3961 C C2 . MAL B 2 . ? 1.717 27.407 21.659 1.00 15.58 ? 496 MAL A C2 1
HETATM 3962 C C3 . MAL B 2 . ? 3.103 27.861 21.193 1.00 13.17 ? 496 MAL A C3 1
HETATM 3963 C C4 . MAL B 2 . ? 2.942 28.664 19.909 1.00 11.86 ? 496 MAL A C4 1
HETATM 3964 C C5 . MAL B 2 . ? 2.087 29.904 20.193 1.00 14.42 ? 496 MAL A C5 1
HETATM 3965 C C6 . MAL B 2 . ? 1.720 30.758 18.985 1.00 14.61 ? 496 MAL A C6 1
HETATM 3966 O O1 . MAL B 2 . ? 1.510 29.412 23.067 1.00 18.37 ? 496 MAL A O1 1
HETATM 3967 O O2 . MAL B 2 . ? 1.862 26.661 22.871 1.00 14.82 ? 496 MAL A O2 1
HETATM 3968 O O3 . MAL B 2 . ? 3.882 26.682 20.953 1.00 12.67 ? 496 MAL A O3 1
HETATM 3969 O O4 . MAL B 2 . ? 4.256 29.108 19.514 1.00 10.20 ? 496 MAL A O4 1
HETATM 3970 O O5 . MAL B 2 . ? 0.836 29.453 20.754 1.00 15.61 ? 496 MAL A O5 1
HETATM 3971 O O6 . MAL B 2 . ? 0.983 30.021 17.980 1.00 14.23 ? 496 MAL A O6 1
HETATM 3972 C "C1'" . MAL B 2 . ? -0.216 32.841 24.571 1.00 30.41 ? 496 MAL A "C1'" 1
HETATM 3973 C "C2'" . MAL B 2 . ? -0.638 31.588 25.198 1.00 18.61 ? 496 MAL A "C2'" 1
HETATM 3974 C "C3'" . MAL B 2 . ? 0.057 30.300 24.820 1.00 23.53 ? 496 MAL A "C3'" 1
HETATM 3975 C "C4'" . MAL B 2 . ? 0.869 30.574 23.557 1.00 23.49 ? 496 MAL A "C4'" 1
HETATM 3976 C "C5'" . MAL B 2 . ? 1.885 31.667 23.948 1.00 19.64 ? 496 MAL A "C5'" 1
HETATM 3977 C "C6'" . MAL B 2 . ? 2.823 32.280 22.930 1.00 19.63 ? 496 MAL A "C6'" 1
HETATM 3978 O "O1'" . MAL B 2 . ? -0.827 34.119 24.372 1.00 17.28 ? 496 MAL A "O1'" 1
HETATM 3979 O "O2'" . MAL B 2 . ? -1.067 31.400 26.525 1.00 29.30 ? 496 MAL A "O2'" 1
HETATM 3980 O "O3'" . MAL B 2 . ? -0.875 29.278 24.527 1.00 23.41 ? 496 MAL A "O3'" 1
HETATM 3981 O "O5'" . MAL B 2 . ? 1.198 32.842 24.453 1.00 23.65 ? 496 MAL A "O5'" 1
HETATM 3982 O "O6'" . MAL B 2 . ? 2.048 32.851 21.795 1.00 14.06 ? 496 MAL A "O6'" 1
HETATM 3983 C C1 . MAL C 2 . ? 0.637 30.934 30.966 1.00 11.83 ? 498 MAL A C1 1
HETATM 3984 C C2 . MAL C 2 . ? 0.877 32.416 30.689 1.00 11.42 ? 498 MAL A C2 1
HETATM 3985 C C3 . MAL C 2 . ? 0.888 32.751 29.223 1.00 11.41 ? 498 MAL A C3 1
HETATM 3986 C C4 . MAL C 2 . ? 1.807 31.804 28.458 1.00 11.73 ? 498 MAL A C4 1
HETATM 3987 C C5 . MAL C 2 . ? 1.279 30.365 28.741 1.00 11.17 ? 498 MAL A C5 1
HETATM 3988 C C6 . MAL C 2 . ? 2.220 29.309 28.065 1.00 12.00 ? 498 MAL A C6 1
HETATM 3989 O O1 . MAL C 2 . ? -0.715 30.580 30.804 1.00 12.37 ? 498 MAL A O1 1
HETATM 3990 O O2 . MAL C 2 . ? -0.104 33.179 31.390 1.00 11.56 ? 498 MAL A O2 1
HETATM 3991 O O3 . MAL C 2 . ? 1.332 34.081 29.100 1.00 10.77 ? 498 MAL A O3 1
HETATM 3992 O O4 . MAL C 2 . ? 1.656 32.017 27.022 1.00 10.76 ? 498 MAL A O4 1
HETATM 3993 O O5 . MAL C 2 . ? 1.442 30.111 30.145 1.00 12.17 ? 498 MAL A O5 1
HETATM 3994 O O6 . MAL C 2 . ? 3.616 29.501 28.336 1.00 10.59 ? 498 MAL A O6 1
HETATM 3995 C "C1'" . MAL C 2 . ? -3.464 28.664 33.250 1.00 14.75 ? 498 MAL A "C1'" 1
HETATM 3996 C "C2'" . MAL C 2 . ? -3.231 30.138 33.496 1.00 14.62 ? 498 MAL A "C2'" 1
HETATM 3997 C "C3'" . MAL C 2 . ? -2.624 30.770 32.246 1.00 13.99 ? 498 MAL A "C3'" 1
HETATM 3998 C "C4'" . MAL C 2 . ? -1.351 29.988 31.943 1.00 13.33 ? 498 MAL A "C4'" 1
HETATM 3999 C "C5'" . MAL C 2 . ? -1.675 28.518 31.699 1.00 15.36 ? 498 MAL A "C5'" 1
HETATM 4000 C "C6'" . MAL C 2 . ? -0.423 27.660 31.535 1.00 15.60 ? 498 MAL A "C6'" 1
HETATM 4001 O "O1'" A MAL C 2 . ? -4.466 28.531 32.350 0.64 17.30 ? 498 MAL A "O1'" 1
HETATM 4002 O "O1'" B MAL C 2 . ? -4.214 27.971 34.112 0.36 17.59 ? 498 MAL A "O1'" 1
HETATM 4003 O "O2'" . MAL C 2 . ? -4.420 30.837 33.809 1.00 17.68 ? 498 MAL A "O2'" 1
HETATM 4004 O "O3'" . MAL C 2 . ? -2.284 32.101 32.588 1.00 13.18 ? 498 MAL A "O3'" 1
HETATM 4005 O "O5'" . MAL C 2 . ? -2.283 28.001 32.888 1.00 15.86 ? 498 MAL A "O5'" 1
HETATM 4006 O "O6'" . MAL C 2 . ? -0.732 26.334 31.256 1.00 17.79 ? 498 MAL A "O6'" 1
http://ftp-versioned.wwpdb.org/pdb_versioned/data/entries/wd/pdb_00001wdq/pdb_00001wdq_xyz_v2-0.cif.gz:
HETATM 3960 C C1 . GLC B 2 . ? -0.216 32.841 24.571 1.00 30.41 ? 1 GLC B C1 1
HETATM 3961 C C2 . GLC B 2 . ? -0.638 31.588 25.198 1.00 18.61 ? 1 GLC B C2 1
HETATM 3962 C C3 . GLC B 2 . ? 0.057 30.300 24.820 1.00 23.53 ? 1 GLC B C3 1
HETATM 3963 C C4 . GLC B 2 . ? 0.869 30.574 23.557 1.00 23.49 ? 1 GLC B C4 1
HETATM 3964 C C5 . GLC B 2 . ? 1.885 31.667 23.948 1.00 19.64 ? 1 GLC B C5 1
HETATM 3965 C C6 . GLC B 2 . ? 2.823 32.280 22.930 1.00 19.63 ? 1 GLC B C6 1
HETATM 3966 O O1 . GLC B 2 . ? -0.827 34.119 24.372 1.00 17.28 ? 1 GLC B O1 1
HETATM 3967 O O2 . GLC B 2 . ? -1.067 31.400 26.525 1.00 29.30 ? 1 GLC B O2 1
HETATM 3968 O O3 . GLC B 2 . ? -0.875 29.278 24.527 1.00 23.41 ? 1 GLC B O3 1
HETATM 3969 O O4 . GLC B 2 . ? 1.510 29.412 23.067 1.00 18.37 ? 1 GLC B O4 1
HETATM 3970 O O5 . GLC B 2 . ? 1.198 32.842 24.453 1.00 23.65 ? 1 GLC B O5 1
HETATM 3971 O O6 . GLC B 2 . ? 2.048 32.851 21.795 1.00 14.06 ? 1 GLC B O6 1
HETATM 3972 C C1 . GLC B 2 . ? 0.923 28.692 21.983 1.00 15.32 ? 2 GLC B C1 1
HETATM 3973 C C2 . GLC B 2 . ? 1.717 27.407 21.659 1.00 15.58 ? 2 GLC B C2 1
HETATM 3974 C C3 . GLC B 2 . ? 3.103 27.861 21.193 1.00 13.17 ? 2 GLC B C3 1
HETATM 3975 C C4 . GLC B 2 . ? 2.942 28.664 19.909 1.00 11.86 ? 2 GLC B C4 1
HETATM 3976 C C5 . GLC B 2 . ? 2.087 29.904 20.193 1.00 14.42 ? 2 GLC B C5 1
HETATM 3977 C C6 . GLC B 2 . ? 1.720 30.758 18.985 1.00 14.61 ? 2 GLC B C6 1
HETATM 3978 O O2 . GLC B 2 . ? 1.862 26.661 22.871 1.00 14.82 ? 2 GLC B O2 1
HETATM 3979 O O3 . GLC B 2 . ? 3.882 26.682 20.953 1.00 12.67 ? 2 GLC B O3 1
HETATM 3980 O O4 . GLC B 2 . ? 4.256 29.108 19.514 1.00 10.20 ? 2 GLC B O4 1
HETATM 3981 O O5 . GLC B 2 . ? 0.836 29.453 20.754 1.00 15.61 ? 2 GLC B O5 1
HETATM 3982 O O6 . GLC B 2 . ? 0.983 30.021 17.980 1.00 14.23 ? 2 GLC B O6 1
HETATM 3983 C C1 . GLC C 2 . ? -3.464 28.664 33.250 1.00 14.75 ? 1 GLC C C1 1
HETATM 3984 C C2 . GLC C 2 . ? -3.231 30.138 33.496 1.00 14.62 ? 1 GLC C C2 1
HETATM 3985 C C3 . GLC C 2 . ? -2.624 30.770 32.246 1.00 13.99 ? 1 GLC C C3 1
HETATM 3986 C C4 . GLC C 2 . ? -1.351 29.988 31.943 1.00 13.33 ? 1 GLC C C4 1
HETATM 3987 C C5 . GLC C 2 . ? -1.675 28.518 31.699 1.00 15.36 ? 1 GLC C C5 1
HETATM 3988 C C6 . GLC C 2 . ? -0.423 27.660 31.535 1.00 15.60 ? 1 GLC C C6 1
HETATM 3989 O O1 A GLC C 2 . ? -4.466 28.531 32.350 0.64 17.30 ? 1 GLC C O1 1
HETATM 3990 O O1 B GLC C 2 . ? -4.214 27.971 34.112 0.36 17.59 ? 1 GLC C O1 1
HETATM 3991 O O2 . GLC C 2 . ? -4.420 30.837 33.809 1.00 17.68 ? 1 GLC C O2 1
HETATM 3992 O O3 . GLC C 2 . ? -2.284 32.101 32.588 1.00 13.18 ? 1 GLC C O3 1
HETATM 3993 O O4 . GLC C 2 . ? -0.715 30.580 30.804 1.00 12.37 ? 1 GLC C O4 1
HETATM 3994 O O5 . GLC C 2 . ? -2.283 28.001 32.888 1.00 15.86 ? 1 GLC C O5 1
HETATM 3995 O O6 . GLC C 2 . ? -0.732 26.334 31.256 1.00 17.79 ? 1 GLC C O6 1
HETATM 3996 C C1 . GLC C 2 . ? 0.637 30.934 30.966 1.00 11.83 ? 2 GLC C C1 1
HETATM 3997 C C2 . GLC C 2 . ? 0.877 32.416 30.689 1.00 11.42 ? 2 GLC C C2 1
HETATM 3998 C C3 . GLC C 2 . ? 0.888 32.751 29.223 1.00 11.41 ? 2 GLC C C3 1
HETATM 3999 C C4 . GLC C 2 . ? 1.807 31.804 28.458 1.00 11.73 ? 2 GLC C C4 1
HETATM 4000 C C5 . GLC C 2 . ? 1.279 30.365 28.741 1.00 11.17 ? 2 GLC C C5 1
HETATM 4001 C C6 . GLC C 2 . ? 2.220 29.309 28.065 1.00 12.00 ? 2 GLC C C6 1
HETATM 4002 O O2 . GLC C 2 . ? -0.104 33.179 31.390 1.00 11.56 ? 2 GLC C O2 1
HETATM 4003 O O3 . GLC C 2 . ? 1.332 34.081 29.100 1.00 10.77 ? 2 GLC C O3 1
HETATM 4004 O O4 . GLC C 2 . ? 1.656 32.017 27.022 1.00 10.76 ? 2 GLC C O4 1
HETATM 4005 O O5 . GLC C 2 . ? 1.442 30.111 30.145 1.00 12.17 ? 2 GLC C O5 1
HETATM 4006 O O6 . GLC C 2 . ? 3.616 29.501 28.336 1.00 10.59 ? 2 GLC C O6 1
| pdb_00001wdq_xyz_v1-2.cif.gz | pdb_00001wdq_xyz_v2-0.cif.gz |
 |  |
Issue: Outdated PISA dataset (e.g 2aw3)? - with outdated struct_asym_id
| chem_comp_ids | entity_id | in_chains | in_struct_asyms | length | molecule_name | molecule_type | number_of_copies | pdb_id |
|---|---|---|---|---|---|---|---|---|
| 1 | [“A”,”B”] | [“A”,”B”] | 796 | [“Maltodextrin phosphorylase”] | polypeptide(L) | 2 | 2aw3 | |
| [“BGC”,”GLC”] | 2 | [“C”,”D”] | [“C”,”D”] | [“alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose”] | carbohydrate polymer | 10 | 2aw3 | |
| [“SO4”] | 3 | [“A”,”B”] | [“E”,”G”] | [“SULFATE ION”] | bound | 2 | 2aw3 | |
| [“PLP”] | 4 | [“A”,”B”] | [“F”,”H”] | [“PYRIDOXAL-5’-PHOSPHATE”] | bound | 2 | 2aw3 | |
| [“HOH”] | 5 | [“A”,”B”] | [“I”,”J”] | [“water”] | water | 1162 | 2aw3 |
provided by https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/2aw3
| structure_1.range | structure_2.range | css | delta_g_interface | structure_2.symmetry_operator |
|---|---|---|---|---|
| B | A | 0.439004 | -19.4029 | x,y,z |
| B | A | 0 | -2.16533 | -x,y-1/2,-z+1/2 |
| A | B | 0 | 1.03891 | -x,y-1/2,-z+1/2 |
| A | B | 0 | -1.80886 | -x+1,y-1/2,-z+1/2 |
| A | A | 0 | 0.111518 | x-1/2,-y+1/2,-z+1 |
| [PLP]E:900 | A | 0.094355 | -0.23042 | x,y,z |
| [PLP]H:900 | B | 0.094355 | -0.36542 | x,y,z |
| A | A | 0 | 0.124812 | x-1,y,z |
| [GLC]F:995 | B | 0 | 2.50296 | x,y,z |
| [GLC]C:995 | A | 0 | 2.52312 | x,y,z |
| [GLC]F:996 | B | 0 | 3.2986 | x,y,z |
| [GLC]C:996 | A | 0 | 3.22187 | x,y,z |
| B | A | 0 | 3.66116 | -x+1/2,-y,z-1/2 |
| [GLC]C:998 | A | 0.025217 | 3.01159 | x,y,z |
| [GLC]F:998 | B | 0.025217 | 2.95375 | x,y,z |
| [GLC]C:997 | A | 0 | 2.45925 | x,y,z |
| [GLC]F:997 | B | 0 | 2.37176 | x,y,z |
| [BGC]F:994 | B | 0 | 1.2581 | x,y,z |
| [BGC]C:994 | A | 0 | 0.920195 | x,y,z |
| B | A | 0 | -2.43397 | -x+1,y-1/2,-z+1/2 |
| B | B | 0 | 1.02116 | x-1,y,z |
| [SO4]G:2999 | B | 0.382227 | -9.9445 | x,y,z |
| [SO4]D:1999 | A | 0.382227 | -10.0581 | x,y,z |
| [GLC]C:995 | [BGC]C:994 | 0 | 1.52676 | x,y,z |
| [GLC]F:995 | [BGC]F:994 | 0 | 1.42288 | x,y,z |
| [GLC]F:996 | [GLC]F:995 | 0 | 1.32526 | x,y,z |
| [GLC]C:996 | [GLC]C:995 | 0 | 1.28204 | x,y,z |
| [GLC]C:997 | [GLC]C:996 | 0 | 1.29394 | x,y,z |
| [GLC]F:997 | [GLC]F:996 | 0 | 1.27743 | x,y,z |
| B | B | 0 | 0.207328 | -x,y-1/2,-z+1/2 |
| [GLC]F:998 | [GLC]F:997 | 0 | 0.761414 | x,y,z |
| [GLC]C:998 | [GLC]C:997 | 0 | 0.682544 | x,y,z |
| [SO4]G:2999 | [GLC]F:998 | 0.101796 | -3.32977 | x,y,z |
| [SO4]D:1999 | [GLC]C:998 | 0.101796 | -3.06167 | x,y,z |
| [PLP]H:900 | [SO4]G:2999 | 0.131857 | -4.28057 | x,y,z |
| [PLP]E:900 | [SO4]D:1999 | 0.131857 | -3.99833 | x,y,z |
| [SO4]G:2999 | [GLC]F:997 | 0.094466 | -2.95927 | x,y,z |
| [SO4]D:1999 | [GLC]C:997 | 0.094466 | -2.97197 | x,y,z |
| [PLP]H:900 | [GLC]F:998 | 0.017104 | -0.56505 | x,y,z |
| [PLP]E:900 | [GLC]C:998 | 0.017104 | -0.50888 | x,y,z |
| [GLC]C:997 | [GLC]C:995 | 0 | 0.011675 | x,y,z |
| [GLC]F:997 | [GLC]F:995 | 0 | 0.004026 | x,y,z |
| [GLC]F:996 | [BGC]F:994 | 0 | 0.004843 | x,y,z |
| [GLC]C:996 | [BGC]C:994 | 0 | 0.006433 | x,y,z |
| [GLC]C:998 | [GLC]C:996 | 0 | 0.013314 | x,y,z |
| [GLC]F:998 | [GLC]F:996 | 0 | 0.003201 | x,y,z |
provided by https://www.ebi.ac.uk/pdbe/api/pisa/interfacelist/2aw3/0
Related Issues
- https://github.com/biojava/biojava/pull/868: Minimal read support for files with ‘branched’ entities