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
- 4DX6
- Type
- protein
- Length
- 3,419 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acriflavine resistance protein B; Darpin
- UniProt
- P31224
- 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 | Acriflavine resistance protein B | protein | 1044 | 52% helix, 18% strand | P31224 |
| B | Acriflavine resistance protein B | protein | 1033 | 54% helix, 19% strand | P31224 |
| C | Acriflavine resistance protein B | protein | 1034 | 54% helix, 19% strand | P31224 |
| D | Darpin | protein | 156 | 56% helix, 0% strand | — |
| E | Darpin | protein | 152 | 53% helix, 0% strand | — |
Ligands and binding sites
- LMT · Dodecyl-beta-D-maltoside · additive · 7 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 | 703 | 0.86 | 0.90 | 87 | empty |
| 2 | 691 | 0.86 | 0.90 | 72 | empty |
| 3 | 950 | 0.83 | 0.84 | 85 | empty |
| 4 | 568 | 0.81 | 0.87 | 40 | empty |
| 5 | 509 | 0.80 | 0.88 | 73 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3550 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 3300 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 3054 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 930 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 818 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4DX6 · 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 4DX6 · PDBe 4DX6 · UniProt P31224
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