MolNFT v1 · #57958 · protein
Structures of the multidrug exporter acrb reveal a proximal multisite drug-binding pocket
3AOD · Acriflavine resistance protein B: “Structures of the multidrug exporter acrb reveal a proximal multisite drug-binding pocket”. X-ray diffraction, 2 ligands (MIY, RFP), 20 pockets (best druggability 0.85). MolNFT v1 #57958 on…
- PDB
- 3AOD
- Type
- protein
- Length
- 3,066 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B
- UniProt
- P31224
- Ligands
- MIY, RFP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acriflavine resistance protein B | protein | 1022 | 46% helix, 15% strand | P31224 |
Ligands and binding sites
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains A
- RFP · Rifampicin · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.85 | 0.90 | 87 | empty |
| 2 | 548 | 0.85 | 0.91 | 92 | empty |
| 3 | 973 | 0.84 | 0.85 | 121 | MIY |
| 4 | 453 | 0.82 | 0.90 | 60 | empty |
| 5 | 1134 | 0.81 | 0.82 | 146 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3562 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3282 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2987 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3AOD · Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket · 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 B against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 3AOD · PDBe 3AOD · UniProt P31224
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