Research workbench
Crystal structure of E.COLI bama beta-barrel in complex with darobactin (crystal form 2)
Analyse Crystal structure of E.COLI bama beta-barrel in complex with darobactin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NRF
- 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; Darobactin
- UniProt
- P0A942
- Ligands
- MG
- Pockets
- 3 · best druggability 0.68
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 | Darobactin | protein | 7 | 0% helix, 71% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.68 | 0.77 | 66 | empty |
| 2 | 377 | 0.63 | 0.78 | 38 | empty |
| 3 | 103 | 0.46 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7NRF · Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2) · 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 7NRF · PDBe 7NRF · UniProt P0A942
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