Research workbench
BDM88832 inhibitor bound to the transmembrane domain of acrb-R971A
Analyse BDM88832 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
- 7OUL
- Type
- protein
- Length
- 3,408 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
- 1KE, D12, LPX, DDQ, C14, SO4
- Pockets
- 20 · best druggability 0.88
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 | 1032 | 53% helix, 19% strand | P31224 |
| B | Multidrug efflux pump subunit acrb | protein | 1034 | 55% 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
- 1KE · 1-(3-chloranyl-5-iodanyl-pyridin-2-yl)piperazine · ligand · chains A
- D12 · Dodecane · ligand · chains A
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains B, C
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · chains C
- C14 · Tetradecane · ligand · chains B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, C, B
- GOL · Glycerol · additive · 2 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 | 645 | 0.88 | 0.93 | 108 | EDO, GOL |
| 2 | 673 | 0.86 | 0.91 | 85 | empty |
| 3 | 1011 | 0.84 | 0.85 | 96 | empty |
| 4 | 1029 | 0.83 | 0.85 | 92 | SO4 |
| 5 | 529 | 0.82 | 0.88 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3532 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 3403 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3188 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 911 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 890 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7OUL · BDM88832 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 7OUL · PDBe 7OUL · UniProt P31224
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.