MolNFT v1 · #112380 · protein
Crystal structure of acrb in complex with antibiotic in P21 space group
4ZJL · Multidrug efflux pump subunit acrb: “Crystal structure of acrb in complex with antibiotic in P21 space group”. X-ray diffraction, 2 ligands (ERY, NI), 20 pockets (best druggability 0.87). MolNFT v1 #112380 on GenesisL1: 3D…
- PDB
- 4ZJL
- Type
- protein
- Length
- 6,255 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 0.87
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit acrb | protein | 1044 | 52% helix, 20% strand | P31224 |
| B, C, D, E | Multidrug efflux pump subunit acrb | protein | 1042 | 52% helix, 19% strand | P31224 |
| F | Multidrug efflux pump subunit acrb | protein | 1043 | 51% 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 | 899 | 0.87 | 0.89 | 99 | empty |
| 2 | 716 | 0.86 | 0.90 | 88 | empty |
| 3 | 874 | 0.86 | 0.88 | 88 | empty |
| 4 | 851 | 0.86 | 0.89 | 102 | empty |
| 5 | 864 | 0.86 | 0.88 | 87 | ERY |
Interfaces
8 interfaces between chains.
- A–B · 3554 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 3483 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3375 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 3368 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 3009 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4ZJL · Crystal structure of AcrB in complex with antibiotic in P21 space group · the same entry in another collection · chain F against F, 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 0.98
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 4ZJL · PDBe 4ZJL · UniProt P31224
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