› 4dfu

X-ray diffraction
1.98Å resolution

Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA in complex with kanamycin inhibited with quercetin

Released:
DOI: 10.2210/pdb4dfu/pdb
PDB entry 4dfu coloured by chain, front view.
PDB entry 4dfu coloured by chain, side view.
PDB entry 4dfu coloured by chain, top view.
Source organism: Enterococcus casseliflavus
Primary publication:
A small molecule discrimination map of the antibiotic resistance kinome.
Shakya T, Stogios PJ, Waglechner N, Evdokimova E, Ejim L, Blanchard JE, McArthur AG, Savchenko A, Wright GD
Chem Biol 18 1591-601 (2011)
PMID: 22195561

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130603 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminoglycoside phosphotransferase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 322 amino acids
Theoretical weight: 38.28 KDa
Source organism: Enterococcus casseliflavus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68183 (Residues: 1-301; Coverage: 100%)
Gene name: aph(2'')-Id
Sequence domains: Phosphotransferase enzyme family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand KAN 2 x KAN
Ligand QUE 3 x QUE
Ligand CL 2 x CL
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 43.141Å b: 101.814Å c: 70.249Å
α: 90° β: 96.86° γ: 90°
R-values:
R R work R free
0.222 0.219 0.27
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

Drug combinations: a strategy to extend the life of antibiotics in the 21st century.
Tyers et al. (2019)
13 more

3 mentions without citation

Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections.
Labby et al. (2013)
2 more