› 3i3y

X-ray diffraction
2.15Å resolution

Crystal structure of Ribokinase in Complex with D-Ribose from Klebsiella pneumoniae

Released:
DOI: 10.2210/pdb3i3y/pdb
PDB entry 3i3y coloured by chain, front view.
PDB entry 3i3y coloured by chain, side view.
PDB entry 3i3y coloured by chain, top view.
Source organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Entry authors: Satyanarayana L, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
ATP + D-ribose = ADP + D-ribose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108053 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribokinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 299 amino acids
Theoretical weight: 32.05 KDa
Source organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression system: Escherichia coli
UniProt:
  • Canonical: A6T989 (Residues: 2-289; Coverage: 99%)
Gene names: KPN_01729, rbsK
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand GOL 1 x GOL
Ligand RIB 1 x RIB
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 54.488Å b: 105.9Å c: 121.152Å
α: 90° β: 99.45° γ: 90°
R-values:
R R work R free
0.244 0.244 0.276
Expression system: Escherichia coli

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