MolNFT v1 · #184753 · protein
Crystal structure of E.COLI bama beta-barrel in complex with darobactin B
7P1C · Outer membrane protein assembly factor bama: “Crystal structure of E.COLI bama beta-barrel in complex with darobactin B”. X-ray diffraction, 4 pockets (best druggability 0.74). MolNFT v1 #184753 on GenesisL1: 3D structure, binding…
- PDB
- 7P1C
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein assembly factor bama; TRP-asn-UX8-thr-lys-arg-phe
- UniProt
- P0A942
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein assembly factor bama | protein | 368 | 5% helix, 55% strand | P0A942 |
| B | TRP-asn-UX8-thr-lys-arg-phe | protein | 7 | 0% helix, 57% strand | — |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.74 | 0.78 | 94 | empty |
| 2 | 52 | 0.70 | 0.98 | 25 | empty |
| 3 | 92 | 0.46 | 0.80 | 20 | empty |
| 4 | 51 | 0.42 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7P1C · Crystal structure of E.coli BamA beta-barrel in complex with darobactin B · 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 7P1C · PDBe 7P1C · UniProt P0A942
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