Research workbench
Transport of drugs by the multidrug transporter acrb involves an access and a deep binding pocket that are separated by a switch-loop
Analyse Transport of drugs by the multidrug transporter acrb involves an access and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DX5
- Type
- protein
- Length
- 3,418 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B; Darpin
- UniProt
- P31224
- Ligands
- D10, D12, MIY, C14, LMU, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acriflavine resistance protein B | protein | 1044 | 54% helix, 19% strand | P31224 |
| B, C | Acriflavine resistance protein B | protein | 1033 | 55% helix, 19% strand | P31224 |
| D | Darpin | protein | 156 | 54% helix, 0% strand | — |
| E | Darpin | protein | 152 | 53% helix, 0% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 6 copies · chains A, B, C
- D12 · Dodecane · ligand · 4 copies · chains A, B, C
- 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
- C14 · Tetradecane · ligand · chains B, C
- LMU · Dodecyl-alpha-D-maltoside · ligand · chains B
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, C, B
- OCT · N-octane · additive · 7 copies · chains A, C, B
- HEX · Hexane · additive · 5 copies · chains A, B, C
- DD9 · nonane · additive · chains C
- UND · Undecane · additive · chains 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 | 788 | 0.88 | 0.91 | 100 | GOL |
| 2 | 1085 | 0.86 | 0.87 | 120 | GOL |
| 3 | 622 | 0.85 | 0.90 | 75 | empty |
| 4 | 691 | 0.83 | 0.87 | 84 | empty |
| 5 | 397 | 0.82 | 0.90 | 63 | GOL |
Interfaces
7 interfaces between chains.
- A–B · 3512 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 3262 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2966 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 866 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 821 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4DX5 · Transport of drugs by the multidrug transporter AcrB involves an access and a deep… · 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 4DX5 · PDBe 4DX5 · UniProt P31224
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