MolNFT v1 · #107391 · protein
Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump acrb
4U8Y · Multidrug efflux pump subunit acrb: “Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux…”. X-ray diffraction, 1 ligand (MIY), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4U8Y
- Type
- protein
- Length
- 3,418 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb; Darpin
- UniProt
- P31224
- Ligands
- MIY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 16% 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 | 52% 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 · 4 copies · chains A, C, B
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 | 773 | 0.87 | 0.91 | 91 | empty |
| 2 | 889 | 0.85 | 0.87 | 101 | MIY |
| 3 | 643 | 0.85 | 0.90 | 88 | empty |
| 4 | 533 | 0.82 | 0.88 | 45 | empty |
| 5 | 561 | 0.81 | 0.87 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3561 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 3313 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2952 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 859 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 842 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4U8Y · 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 4U8Y · PDBe 4U8Y · UniProt P31224
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