MolNFT v1 · #89119 · protein
Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-iva in complex with kanamycin inhibited with quercetin
4DFU: “Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase…”. X-ray diffraction, 3 ligands (QUE, KAN, CL), 12 pockets (best druggability 0.80). MolNFT v1 #89119 on GenesisL1: 3D structure…
- PDB
- 4DFU
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2")-id
- UniProt
- O68183
- Ligands
- QUE, KAN, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APH(2")-id | protein | 296 | 47% helix, 15% strand | O68183 |
| B | APH(2")-id | protein | 297 | 47% helix, 15% strand | O68183 |
Ligands and binding sites
- QUE · 3,5,7,3',4'-pentahydroxyflavone · ligand · 3 copies · chains A, B
- KAN · Kanamycin A · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.80 | 0.89 | 58 | QUE |
| 2 | 236 | 0.76 | 0.90 | 39 | empty |
| 3 | 216 | 0.66 | 0.84 | 31 | QUE |
| 4 | 139 | 0.64 | 0.87 | 30 | QUE |
| 5 | 56 | 0.56 | 0.89 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1322 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4DFU · Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside… · 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 O68183
- Elsewhere: RCSB PDB 4DFU · PDBe 4DFU · UniProt O68183
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