Research workbench
BDM88855 inhibitor bound to the transmembrane domain of acrb-R971A
Analyse BDM88855 inhibitor bound to the transmembrane domain of acrb-R971A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OUM
- Type
- protein
- Length
- 3,410 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
- D10, DDQ, 1K8, C14, LPX, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit acrb | protein | 1034 | 53% helix, 20% strand | P31224 |
| B | Multidrug efflux pump subunit acrb | protein | 1034 | 54% helix, 19% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1033 | 54% helix, 19% strand | P31224 |
| D | Darpin | protein | 155 | 55% helix, 0% strand | — |
| E | Darpin | protein | 154 | 55% helix, 0% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 4 copies · chains A, C, B
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains A, C
- 1K8 · 3-chloranyl-2-piperazin-1-yl-quinoline · ligand · 2 copies · chains A, B, C
- C14 · Tetradecane · ligand · chains A
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 7 copies · chains A, C, B
- OCT · N-octane · additive · 4 copies · chains C
- GOL · Glycerol · additive · 3 copies · chains A, B, D, 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 | 628 | 0.86 | 0.90 | 76 | EDO |
| 2 | 712 | 0.84 | 0.88 | 79 | empty |
| 3 | 556 | 0.83 | 0.89 | 84 | EDO |
| 4 | 555 | 0.82 | 0.88 | 47 | EDO |
| 5 | 223 | 0.82 | 0.95 | 46 | GOL, EDO |
Interfaces
7 interfaces between chains.
- A–B · 3567 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 3387 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 3158 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 906 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 903 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7OUM · BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A · 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 7OUM · PDBe 7OUM · UniProt P31224
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