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

X-ray diffraction
1.98Å resolution
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
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Aminoglycoside phosphotransferase domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 15389.38 Å2
Buried surface area: 1503.52 Å2
Dissociation area: 416.45 Å2
Dissociation energy (ΔGdiss): -3.03 kcal/mol
Dissociation entropy (TΔSdiss): 5.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-130603
Assembly 2
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Assembly Name: Aminoglycoside phosphotransferase domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 15884.37 Å2
Buried surface area: 1906.6 Å2
Dissociation area: 420 Å2
Dissociation energy (ΔGdiss): -3.48 kcal/mol
Dissociation entropy (TΔSdiss): 5.15 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-130603

Macromolecules

Aminoglycoside phosphotransferase domain-containing protein
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
Pfam: Phosphotransferase enzyme family
InterPro:
CATH:
Aminoglycoside phosphotransferase domain-containing protein in PDB entry 4dfu, assembly 1, front view.
Aminoglycoside phosphotransferase domain-containing protein in PDB entry 4dfu, assembly 1, side view.
Aminoglycoside phosphotransferase domain-containing protein in PDB entry 4dfu, assembly 1, top view.
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