MolNFT v1 · #105551 · protein
Crystal structure of AMINOGLYCOSIDE/MULTIDRUG efflux system acrd from salmonella typhimurium
4R86 · Rnd family AMINOGLYCOSIDE/MULTIDRUG efflux pump: “Crystal structure of AMINOGLYCOSIDE/MULTIDRUG efflux system acrd from salmonella typhimurium”. X-ray diffraction, 1 ligand (BR), 6 pockets (best druggability 0.73). MolNFT v1 #105551…
- PDB
- 4R86
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rnd family AMINOGLYCOSIDE/MULTIDRUG efflux pump
- UniProt
- Q8ZN77
- Ligands
- BR
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rnd family AMINOGLYCOSIDE/MULTIDRUG efflux pump | protein | 290 | 34% helix, 33% strand | Q8ZN77 |
| B | Rnd family AMINOGLYCOSIDE/MULTIDRUG efflux pump | protein | 291 | 34% helix, 33% strand | Q8ZN77 |
Ligands and binding sites
- BR · Bromide ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.73 | 0.81 | 54 | empty |
| 2 | 339 | 0.73 | 0.85 | 50 | empty |
| 3 | 321 | 0.72 | 0.85 | 52 | empty |
| 4 | 145 | 0.53 | 0.80 | 28 | empty |
| 5 | 75 | 0.49 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4R86 · Crystal Structure of Aminoglycoside/Multidrug Efflux System AcrD from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8ZN77
- Elsewhere: RCSB PDB 4R86 · PDBe 4R86 · UniProt Q8ZN77
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