MolNFT v1 · #40953 · protein
Drug export pathway of multidrug exporter acrb revealed by darpin inhibitors
2J8S · Acriflavine resistance protein B: “Drug export pathway of multidrug exporter acrb revealed by darpin inhibitors”. X-ray diffraction, 1 ligand (LMU), 20 pockets (best druggability 0.88). MolNFT v1 #40953 on GenesisL1: 3D structure…
- PDB
- 2J8S
- Type
- protein
- Length
- 3,426 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B; Darpin
- UniProt
- P31224
- Ligands
- LMU
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acriflavine resistance protein B | protein | 1044 | 52% helix, 20% strand | P31224 |
| B | Acriflavine resistance protein B | protein | 1033 | 53% helix, 19% strand | P31224 |
| C | Acriflavine resistance protein B | protein | 1040 | 52% helix, 19% strand | P31224 |
| D | Darpin | protein | 156 | 53% helix, 0% strand | — |
| E | Darpin | protein | 153 | 52% helix, 0% strand | — |
Ligands and binding sites
- LMU · Dodecyl-alpha-D-maltoside · ligand · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 10 copies · chains A, C, B
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 | 839 | 0.88 | 0.91 | 105 | empty |
| 2 | 736 | 0.84 | 0.87 | 85 | empty |
| 3 | 558 | 0.82 | 0.88 | 80 | empty |
| 4 | 664 | 0.82 | 0.86 | 49 | empty |
| 5 | 1118 | 0.80 | 0.82 | 99 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3495 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 3315 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2980 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 952 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 794 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2J8S · Drug Export Pathway of Multidrug Exporter AcrB Revealed by DARPin Inhibitors · the same entry in another collection · chain E against E, 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 C 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 P31224
- Elsewhere: RCSB PDB 2J8S · PDBe 2J8S · UniProt P31224
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