4eum

X-ray diffraction
1.8Å resolution

Crystal structure of a sugar kinase (Target EFI-502132) from Oceanicola granulosus with bound AMP, crystal form II

Released:
Entry authors: Vetting MW, Toro R, Bhosle R, Al Obaidi NF, Morisco LL, Wasserman SR, Sojitra S, Washington E, Scott Glenn A, Chowdhury S, Evans B, Hammonds J, Hillerich B, Love J, Seidel RD, Imker HJ, Gerlt JA, Almo SC, Enzyme Function Initiative (EFI)

Function and Biology Details

Reaction catalysed:
ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173375 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
KDG kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 328 amino acids
Theoretical weight: 34.61 KDa
Source organism: Oceanicola granulosus HTCC2516
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2CIP5 (Residues: 1-305; Coverage: 100%)
Gene name: OG2516_05533
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 79.54Å b: 49.528Å c: 83.267Å
α: 90° β: 101.5° γ: 90°
R-values:
R R work R free
0.179 0.176 0.221
Expression system: Escherichia coli BL21(DE3)