MolNFT v1 · #164088 · protein
Bamabcde in MSP1D1 nanodisc
6SMX · Outer membrane protein assembly factor bama: “Bamabcde in MSP1D1 nanodisc”. Electron microscopy, 11 pockets (best druggability 0.74). MolNFT v1 #164088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SMX
- Type
- protein
- Length
- 1,518 residues
- Chains
- 5
- 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
- B7MBF8, A0A2S5ZNM3, A0A4T5IPK3, P0AC04, P0A938
- Pockets
- 11 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 783 | 16% helix, 37% strand | B7MBF8 |
| B | Outer membrane protein assembly factor bamb | protein | 371 | 1% helix, 36% strand | A0A2S5ZNM3 |
| C | Outer membrane protein assembly factor bamc | protein | 59 | 12% helix, 0% strand | A0A4T5IPK3 |
| D | Outer membrane protein assembly factor bamd | protein | 218 | 73% helix, 0% strand | P0AC04 |
| E | Outer membrane protein assembly factor bame | protein | 87 | 16% helix, 38% strand | P0A938 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.74 | 0.78 | 72 | empty |
| 2 | 624 | 0.72 | 0.79 | 55 | empty |
| 3 | 142 | 0.62 | 0.85 | 35 | empty |
| 4 | 355 | 0.60 | 0.77 | 51 | empty |
| 5 | 268 | 0.55 | 0.76 | 39 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2607 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1329 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 795 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 720 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6SMX · BamABCDE in MSP1D1 nanodisc · the same entry in another collection · chain E against E, TM-score 1.00
- P0AC04 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC04) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P0A938 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A938) · a predicted model of the same protein · chain E against A, TM-score 0.80
- B7MBF8 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (B7MBF8) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 B7MBF8
- Every structure of UniProt A0A2S5ZNM3
- Every structure of UniProt A0A4T5IPK3
- Every structure of UniProt P0AC04
- Every structure of UniProt P0A938
- Elsewhere: RCSB PDB 6SMX · PDBe 6SMX · UniProt B7MBF8 · UniProt A0A2S5ZNM3 · UniProt A0A4T5IPK3 · UniProt P0AC04 · UniProt P0A938
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