MolNFT v1 · #112383 · protein
Crystal structure of acrb triple mutant in complex with antibiotic in P21 space group
4ZJO · Multidrug efflux pump subunit acrb: “Crystal structure of acrb triple mutant in complex with antibiotic in P21 space group”. X-ray diffraction, 2 ligands (ERY, NI), 20 pockets (best druggability 0.85). MolNFT v1 #112383 on…
- PDB
- 4ZJO
- Type
- protein
- Length
- 6,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb
- UniProt
- P31224
- Ligands
- ERY, NI
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Multidrug efflux pump subunit acrb | protein | 1042 | 53% helix, 20% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1044 | 52% helix, 19% strand | P31224 |
| F | Multidrug efflux pump subunit acrb | protein | 1046 | 52% helix, 19% strand | P31224 |
Ligands and binding sites
- ERY · Erythromycin A · ligand · 2 copies · chains A, D
- NI · Nickel (II) ion · metal · 3 copies · chains A, C, E
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, B, C, D, E, F
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 | 913 | 0.85 | 0.87 | 88 | empty |
| 2 | 800 | 0.85 | 0.88 | 90 | empty |
| 3 | 857 | 0.85 | 0.87 | 80 | empty |
| 4 | 773 | 0.84 | 0.88 | 80 | empty |
| 5 | 603 | 0.83 | 0.88 | 94 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3519 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 3425 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 3374 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 3292 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2941 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 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 0.98
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 4ZJO · PDBe 4ZJO · UniProt P31224
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