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Crystal structure of acrb deletion mutant in complex with antibiotic in P21 space group
Analyse Crystal structure of acrb deletion mutant in complex with antibiotic in P21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZJQ
- Type
- protein
- Length
- 6,223 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 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Multidrug efflux pump subunit acrb | protein | 1038 | 53% helix, 20% strand | P31224 |
| B, E, F | Multidrug efflux pump subunit acrb | protein | 1037 | 53% helix, 19% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1036 | 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 | 1083 | 0.86 | 0.87 | 132 | empty |
| 2 | 827 | 0.85 | 0.88 | 88 | empty |
| 3 | 970 | 0.85 | 0.86 | 111 | empty |
| 4 | 702 | 0.85 | 0.88 | 89 | empty |
| 5 | 905 | 0.85 | 0.87 | 81 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3474 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 3447 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 3378 Ų buried · 33 hydrogen bonds · protein-protein
- D–F · 3326 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2911 Ų buried · 27 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 4ZJQ · PDBe 4ZJQ · UniProt P31224
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