› 4gki

X-ray diffraction
1.88Å resolution

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NM-PP1

Released:
DOI: 10.2210/pdb4gki/pdb
PDB entry 4gki coloured by chain, front view.
PDB entry 4gki coloured by chain, side view.
PDB entry 4gki coloured by chain, top view.
Source organism: Acinetobacter baumannii AYE
Primary publication:
Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance.
Stogios PJ, Spanogiannopoulos P, Evdokimova E, Egorova O, Shakya T, Todorovic N, Capretta A, Wright GD, Savchenko A
Biochem J 454 191-200 (2013)
PMID: 23758273

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-241372 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminoglycoside 3'-phosphotransferase AphA1-IAB Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 272 amino acids
Theoretical weight: 31.35 KDa
Source organism: Acinetobacter baumannii AYE
Expression system: Escherichia coli BL21(DE3)
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand KAN 12 x KAN
Ligand 0JN 12 x 0JN
Ligand NA 14 x NA
Ligand CL 1 x CL
Ligand ACT 28 x ACT
Ligand PEG 6 x PEG
1 modified residue:
Ligand MSE 84 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P1
Unit cell:
a: 96.843Å b: 97.103Å c: 112.128Å
α: 103.24° β: 106.18° γ: 112.66°
R-values:
R R work R free
0.168 0.166 0.216
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

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

5 mentions without citation

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