Research workbench
Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Analyse Coupling of remote alternating-access transport mechanisms for protons and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U95
- Type
- protein
- Length
- 3,418 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Escherichia coli; synthetic construct
- Molecule
- Multidrug efflux pump subunit AcrB; DARPin
- UniProt
- P31224
- Ligands
- MIY
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit AcrB | protein | 1044 | 53% helix, 19% strand | P31224 |
| B, C | Multidrug efflux pump subunit AcrB | protein | 1033 | 54% helix, 19% strand | P31224 |
| D | DARPin | protein | 156 | 54% helix, 0% strand | — |
| E | DARPin | protein | 152 | 51% helix, 0% strand | — |
Ligands and binding sites
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains B
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A, B, C
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 | 933 | 0.88 | 0.89 | 122 | empty |
| 2 | 747 | 0.87 | 0.91 | 91 | empty |
| 3 | 1200 | 0.85 | 0.86 | 139 | empty |
| 4 | 629 | 0.85 | 0.89 | 90 | MIY |
| 5 | 676 | 0.83 | 0.87 | 85 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3508 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 3356 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2982 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 852 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 846 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4U95 · Coupling of remote alternating-access transport mechanisms for protons and substrates in… · the same entry in another collection · chain E against E, 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 0.99
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 4U95 · PDBe 4U95 · UniProt P31224
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