› 3ikh

X-ray diffraction
1.88Å resolution

Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae

Released:
DOI: 10.2210/pdb3ikh/pdb
PDB entry 3ikh coloured by chain, front view.
PDB entry 3ikh coloured by chain, side view.
PDB entry 3ikh 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 BL21(DE3)
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

2 bound ligands:
Ligand ATP 4 x ATP
Ligand GOL 2 x GOL
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: 54.332Å b: 106.352Å c: 122.056Å
α: 90° β: 99.51° γ: 90°
R-values:
R R work R free
0.235 0.22 0.24
Expression system: Escherichia coli BL21(DE3)

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