Research workbench
Structure of a BAM/ESPP(BETA9-12) hybrid-barrel intermediate
Analyse Structure of a BAM/ESPP(BETA9-12) hybrid-barrel intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RI4
- Type
- protein
- Length
- 1,578 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ESPPBETA9-12; Outer membrane protein assembly factor bama; Outer membrane protein…
- UniProt
- P0A940, A0A507WQ69, W8SZY2, C3SYV7, A0A3L5AP29
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 16% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | ESPPBETA9-12 | protein | 54 | 0% helix, 9% strand | — |
| A | Outer membrane protein assembly factor bama | protein | 783 | 15% helix, 27% strand | P0A940 |
| B | Outer membrane protein assembly factor bamb | protein | 371 | 1% helix, 19% strand | A0A507WQ69 |
| C | Outer membrane protein assembly factor bamc | protein | 61 | 0% helix, 0% strand | W8SZY2 |
| D | Outer membrane protein assembly factor bamd | protein | 220 | 57% helix, 0% strand | C3SYV7 |
| E | Outer membrane protein assembly factor bame | protein | 89 | 9% helix, 26% strand | A0A3L5AP29 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.78 | 0.80 | 96 | empty |
| 2 | 289 | 0.77 | 0.89 | 35 | empty |
| 3 | 1138 | 0.76 | 0.78 | 109 | empty |
| 4 | 86 | 0.63 | 0.90 | 22 | empty |
| 5 | 348 | 0.62 | 0.78 | 42 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2421 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1348 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1261 Ų buried · 15 hydrogen bonds · protein-protein
- G–A · 1224 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 865 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7RI4 · Structure of a BAM/EspP(beta9-12) hybrid-barrel intermediate · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.87
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 A0A507WQ69
- Every structure of UniProt W8SZY2
- Every structure of UniProt C3SYV7
- Every structure of UniProt A0A3L5AP29
- Elsewhere: RCSB PDB 7RI4 · PDBe 7RI4 · UniProt P0A940 · UniProt A0A507WQ69 · UniProt W8SZY2 · UniProt C3SYV7 · UniProt A0A3L5AP29
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