MolNFT v1 · #161517 · protein
Crystal structure of E.COLI bama beta-barrel in complex with nanobody E6
6QGW · Outer membrane protein assembly factor bama: “Crystal structure of E.COLI bama beta-barrel in complex with nanobody E6”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #161517 on GenesisL1: 3D structure, binding…
- PDB
- 6QGW
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; NANOE6
- UniProt
- P0A942
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 364 | 7% helix, 55% strand | P0A942 |
| B | NANOE6 | protein | 122 | 10% helix, 48% strand | — |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 15 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.98 | 24 | empty |
| 2 | 710 | 0.67 | 0.76 | 65 | empty |
| 3 | 418 | 0.61 | 0.77 | 47 | empty |
| 4 | 69 | 0.48 | 0.84 | 17 | empty |
| 5 | 99 | 0.35 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6QGW · Crystal structure of E.coli BamA beta-barrel in complex with nanobody E6 · 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 0.99
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 6QGW · PDBe 6QGW · UniProt P0A942
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