MolNFT v1 · #161519 · protein
Crystal structure of E.COLI bama beta-barrel in complex with nanobody B12
6QGY · Outer membrane protein assembly factor bama: “Crystal structure of E.COLI bama beta-barrel in complex with nanobody B12”. X-ray diffraction, 11 pockets (best druggability 0.80). MolNFT v1 #161519 on GenesisL1: 3D structure, binding…
- PDB
- 6QGY
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; NANOB12
- UniProt
- P0A942
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 369 | 7% helix, 54% strand | P0A942 |
| B | NANOB12 | protein | 121 | 5% helix, 49% strand | — |
| C | Outer membrane protein assembly factor bama | protein | 370 | 6% helix, 54% strand | P0A942 |
| D | NANOB12 | protein | 122 | 7% helix, 47% strand | — |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 10 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.80 | 0.82 | 100 | C8E |
| 2 | 1083 | 0.76 | 0.79 | 95 | empty |
| 3 | 60 | 0.73 | 0.99 | 30 | empty |
| 4 | 58 | 0.71 | 0.98 | 26 | empty |
| 5 | 704 | 0.68 | 0.76 | 60 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1017 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1006 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 461 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 221 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6QGY · Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12 · the same entry in another collection · chain B against B, 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 0.97
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 6QGY · PDBe 6QGY · UniProt P0A942
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