MolNFT v1 · #87535 · protein
Crystal structure of acrb-acrz complex
4C48 · Acriflavine resistance protein B: “Crystal structure of acrb-acrz complex”. X-ray diffraction, 1 ligand (NI), 15 pockets (best druggability 0.78). MolNFT v1 #87535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4C48
- Type
- protein
- Length
- 1,230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B; Darpin; Uncharacterized membrane protein ybht
- UniProt
- P31224, P0AAW9
- Ligands
- NI
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acriflavine resistance protein B | protein | 1032 | 53% helix, 17% strand | P31224 |
| B | Darpin | protein | 152 | 51% helix, 0% strand | — |
| C | Uncharacterized membrane protein ybht | protein | 46 | 74% helix, 0% strand | P0AAW9 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.78 | 0.95 | 35 | empty |
| 2 | 524 | 0.78 | 0.85 | 81 | empty |
| 3 | 518 | 0.76 | 0.83 | 64 | empty |
| 4 | 195 | 0.67 | 0.86 | 27 | empty |
| 5 | 173 | 0.65 | 0.85 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1366 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4C48 · Crystal structure of AcrB-AcrZ complex · the same entry in another collection · chain A against A, TM-score 1.00
- P31224 · AlphaFold monomer V2.0 prediction for multidrug efflux pump subunit acrb (P31224) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P0AAW9 · AlphaFold monomer V2.0 prediction for multidrug efflux pump accessory protein acrz… · a predicted model of the same protein · chain C against A, TM-score 0.72
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 P31224
- Every structure of UniProt P0AAW9
- Elsewhere: RCSB PDB 4C48 · PDBe 4C48 · UniProt P31224 · UniProt P0AAW9
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