› 1rk2

X-ray diffraction
2.25Å resolution

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121

Released:
DOI: 10.2210/pdb1rk2/pdb
PDB entry 1rk2 coloured by chain, front view.
PDB entry 1rk2 coloured by chain, side view.
PDB entry 1rk2 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Induced fit on sugar binding activates ribokinase.
Sigrell JA, Cameron AD, Mowbray SL
J Mol Biol 290 1009-18 (1999)
PMID: 10438599

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141890 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribokinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 309 amino acids
Theoretical weight: 32.32 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A9J6 (Residues: 1-309; Coverage: 100%)
Gene names: JW3731, b3752, rbsK
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

4 bound ligands:
Ligand RIB 4 x RIB
Ligand ALF 4 x ALF
Ligand MG 4 x MG
Ligand ADP 4 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P212121
Unit cell:
a: 55.201Å b: 62.492Å c: 337.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.265
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Pentose phosphates in nucleoside interconversion and catabolism.
Tozzi et al. (2006)
4 more

4 mentions without citation

Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
Zhang et al. (2002)
3 more