Research workbench
Crystal structure of acrb triple mutant in complex with antibiotic in P21 space group
Analyse Crystal structure of acrb triple mutant in complex with antibiotic in P21 space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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