› 1ko5

X-ray diffraction
2.28Å resolution

Crystal structure of gluconate kinase

Released:
DOI: 10.2210/pdb1ko5/pdb
PDB entry 1ko5 coloured by chain, front view.
PDB entry 1ko5 coloured by chain, side view.
PDB entry 1ko5 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.
Kraft L, Sprenger GA, Lindqvist Y
J Mol Biol 318 1057-69 (2002)
PMID: 12054802

Function and Biology Details

Reaction catalysed: 
ATP + D-gluconate = ADP + 6-phospho-D-gluconate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155522 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thermoresistant gluconokinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 175 amino acids
Theoretical weight: 19.57 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46859 (Residues: 1-175; Coverage: 100%)
Gene names: JW3400, b3437, gntK
Sequence domains: Shikimate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P21
Unit cell:
a: 43.274Å b: 89.206Å c: 51.479Å
α: 90° β: 105.14° γ: 90°
R-values:
R R work R free
0.217 0.214 0.277
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.
Wako et al. (2017)
1 more

2 mentions without citation

Distinct Conformation of ATP Molecule in Solution and on Protein.
Kobayashi et al. (2013)
1 more