Research workbench
Crystal structure of acrb in P21 space group
Analyse Crystal structure of acrb in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZIT
- Type
- protein
- Length
- 6,253 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb
- UniProt
- P31224
- Ligands
- NI
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Multidrug efflux pump subunit acrb | protein | 1042 | 52% helix, 20% strand | P31224 |
| B | Multidrug efflux pump subunit acrb | protein | 1043 | 52% helix, 19% strand | P31224 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, C, E
- LMT · Dodecyl-beta-D-maltoside · additive · 6 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 | 997 | 0.87 | 0.89 | 106 | empty |
| 2 | 905 | 0.85 | 0.87 | 125 | empty |
| 3 | 583 | 0.84 | 0.90 | 71 | empty |
| 4 | 612 | 0.84 | 0.89 | 78 | empty |
| 5 | 680 | 0.83 | 0.88 | 87 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3556 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 3487 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 3426 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3245 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3002 Ų buried · 27 hydrogen bonds · protein-protein
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 0.99
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 4ZIT · PDBe 4ZIT · UniProt P31224
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