› 5byf

X-ray diffraction
2Å resolution

Crystal structure of human ribokinase in complex with AMP

Released:
DOI: 10.2210/pdb5byf/pdb
PDB entry 5byf coloured by chain, front view.
PDB entry 5byf coloured by chain, side view.
PDB entry 5byf coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Park J, Chakrabarti J, Singh B, Gupta RS, Junop MS

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-190599 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribokinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 330 amino acids
Theoretical weight: 35.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H477 (Residues: 1-322; Coverage: 100%)
Gene names: RBKS, RBSK
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand AMP 2 x AMP
Ligand NA 4 x NA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 56.09Å b: 63.87Å c: 181.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.222
Expression system: Escherichia coli BL21(DE3)

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