› 6cav

X-ray diffraction
2.6Å resolution

Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin

Released:
DOI: 10.2210/pdb6cav/pdb
PDB entry 6cav coloured by chain, front view.
PDB entry 6cav coloured by chain, side view.
PDB entry 6cav coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2″)-Ia.
Caldwell SJ, Berghuis AM
Antimicrob Agents Chemother 62 (2018)
PMID: 29661878

Function and Biology Details

Reaction catalysed: 
GTP + gentamicin = GDP + gentamicin 2''-phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140902 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional AAC/APH Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 305 amino acids
Theoretical weight: 35.95 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A0C1 (Residues: 175-479; Coverage: 64%)
Gene names: R015, VRA0030, aacA-aphD
Sequence domains: Phosphotransferase enzyme family
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GNP 4 x GNP
Ligand MG 8 x MG
Ligand CL 3 x CL
Ligand 84D 4 x 84D
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 89.99Å b: 98.34Å c: 93.22Å
α: 90° β: 105.24° γ: 90°
R-values:
R R work R free
0.194 0.192 0.244
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding.
Terekhov et al. (2020)
1 more

1 mention without citation

Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2″)-Ia.
Caldwell et al. (2018)