Research workbench
Cryo-EM structure of a substrate-engaged bam complex
Analyse Cryo-EM structure of a substrate-engaged bam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V05
- Type
- protein
- Length
- 1,884 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
- UniProt
- P0A940, P77774, W8SZY2, A0A0H3MJ38, A0A3S5E0E0
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 6 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 758 | 16% helix, 41% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 340 | 1% helix, 37% strand | P77774 |
| C | Outer membrane protein assembly factor bamc | protein | 181 | 20% helix, 25% strand | W8SZY2 |
| D | Outer membrane protein assembly factor bamd | protein | 213 | 76% helix, 0% strand | A0A0H3MJ38 |
| E | Outer membrane protein assembly factor bame | protein | 83 | 16% helix, 33% strand | A0A3S5E0E0 |
| F | Outer membrane protein assembly factor BAMA,OUTER membrane protein assembly factor BAMA,OUTER membrane protein assembly factor BAMA,OUTER membrane protein assembly factor bama | protein | 309 | 2% helix, 49% strand | P0A940 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.76 | 0.79 | 90 | empty |
| 2 | 838 | 0.76 | 0.80 | 85 | empty |
| 3 | 122 | 0.75 | 0.95 | 26 | empty |
| 4 | 123 | 0.71 | 0.92 | 31 | empty |
| 5 | 854 | 0.71 | 0.76 | 78 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2330 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1075 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1038 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 793 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6V05 · Cryo-EM structure of a substrate-engaged Bam complex · the same entry in another collection · chain F against F, TM-score 1.00
- P0A940 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A940) · a predicted model of the same protein · chain F against A, TM-score 0.96
- 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 0.96
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 W8SZY2
- Every structure of UniProt A0A0H3MJ38
- Every structure of UniProt A0A3S5E0E0
- Elsewhere: RCSB PDB 6V05 · PDBe 6V05 · UniProt P0A940 · UniProt P77774 · UniProt W8SZY2 · UniProt A0A0H3MJ38 · UniProt A0A3S5E0E0
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