MolNFT v1 · #161518 · protein
Crystal structure of E.COLI bama beta-barrel in complex with nanobody F7
6QGX · Outer membrane protein assembly factor bama: “Crystal structure of E.COLI bama beta-barrel in complex with nanobody F7”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #161518 on GenesisL1: 3D structure, binding…
- PDB
- 6QGX
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; NANOF7
- UniProt
- P0A942
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 368 | 5% helix, 55% strand | P0A942 |
| B | NANOF7 | protein | 126 | 5% helix, 47% strand | — |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 23 | empty |
| 2 | 691 | 0.68 | 0.76 | 53 | empty |
| 3 | 334 | 0.56 | 0.76 | 45 | empty |
| 4 | 90 | 0.56 | 0.86 | 21 | empty |
| 5 | 247 | 0.54 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6QGX · Crystal structure of E.coli BamA beta-barrel in complex with nanobody F7 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A942 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A942) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A942
- Elsewhere: RCSB PDB 6QGX · PDBe 6QGX · UniProt P0A942
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