Research workbench
Structure of a membrane complex
Analyse Structure of a membrane complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AYW
- Type
- protein
- Length
- 1,489 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
- UniProt
- P0A940, P77774, P0A903, P0AC02, P0A937
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 785 | 15% helix, 42% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 348 | 0% helix, 45% strand | P77774 |
| C | Outer membrane protein assembly factor bamc | protein | 56 | 11% helix, 0% strand | P0A903 |
| D | Outer membrane protein assembly factor bamd | protein | 212 | 73% helix, 0% strand | P0AC02 |
| E | Outer membrane protein assembly factor bame | protein | 88 | 8% helix, 30% strand | P0A937 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.76 | 0.81 | 93 | empty |
| 2 | 1067 | 0.72 | 0.76 | 108 | empty |
| 3 | 57 | 0.71 | 0.98 | 24 | empty |
| 4 | 314 | 0.62 | 0.79 | 53 | empty |
| 5 | 417 | 0.60 | 0.76 | 49 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2129 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1559 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1041 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 976 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 683 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5AYW · Structure of a membrane complex · the same entry in another collection · chain E against E, TM-score 1.00
- P77774 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamb (P77774) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P0A940 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A940) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P0AC02 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC02) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P0A937 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A937) · a predicted model of the same protein · chain E against A, TM-score 0.87
- P0A903 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamc (P0A903) · a predicted model of the same protein · chain C against A, TM-score 0.73
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A940
- Every structure of UniProt P77774
- Every structure of UniProt P0A903
- Every structure of UniProt P0AC02
- Every structure of UniProt P0A937
- Elsewhere: RCSB PDB 5AYW · PDBe 5AYW · UniProt P0A940 · UniProt P77774 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937
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