MolNFT v1 · #173712 · protein
Doxycycline bound structure of bacterial efflux pump.
7B8R · Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump…: “Doxycycline bound structure of bacterial efflux pump.”. X-ray diffraction, 1 ligand (DXT), 20 pockets (best druggability 0.88). MolNFT v1 #173712 on GenesisL1: 3D…
- PDB
- 7B8R
- Type
- protein
- Length
- 2,220 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb; Darpin
- UniProt
- P31224
- Ligands
- DXT
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 587 | 34% helix, 35% strand | P31224 |
| B | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 582 | 33% helix, 34% strand | P31224 |
| C | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 586 | 33% helix, 33% strand | P31224 |
| D | Darpin | protein | 156 | 52% helix, 1% strand | — |
| E | Darpin | protein | 157 | 52% helix, 0% strand | — |
| F | Darpin | protein | 152 | 53% helix, 0% strand | — |
Ligands and binding sites
- DXT · (4s,4ar,5s,5ar,6r,12as)-4-(dimethylamino)-3,5,10,12,12A-pentahydroxy-6-methyl-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · 2 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · 5 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.88 | 0.89 | 126 | PEG |
| 2 | 1045 | 0.87 | 0.89 | 120 | empty |
| 3 | 1155 | 0.85 | 0.86 | 132 | empty |
| 4 | 1066 | 0.85 | 0.86 | 102 | DXT |
| 5 | 1186 | 0.85 | 0.86 | 131 | empty |
Interfaces
9 interfaces between chains.
- B–C · 3117 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3018 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2661 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 873 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 871 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 7B8R · PDBe 7B8R · UniProt P31224
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