› 4ebu

X-ray diffraction
2Å resolution

Crystal structure of a sugar kinase (Target EFI-502312) from Oceanicola granulosus, with bound AMP/ADP crystal form I

Released:
DOI: 10.2210/pdb4ebu/pdb
PDB entry 4ebu coloured by chain, front view.
PDB entry 4ebu coloured by chain, side view.
PDB entry 4ebu coloured by chain, top view.
Source organism: Oceanicola granulosus HTCC2516
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:
Sequence domains:

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 Chain: A
Molecule details ›
Chain: A
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:
Ligand CL 1 x CL
Ligand ADP 1 x ADP
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P3121
Unit cell:
a: 94.308Å b: 94.308Å c: 82.959Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.177 0.215
Expression system: Escherichia coli BL21(DE3)

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