› 1rfu

X-ray diffraction
2.8Å resolution

Crystal structure of pyridoxal kinase complexed with ADP and PLP

Released:
DOI: 10.2210/pdb1rfu/pdb
PDB entry 1rfu coloured by chain, front view.
PDB entry 1rfu coloured by chain, side view.
PDB entry 1rfu coloured by chain, top view.
Source organism: Ovis aries
Primary publication:
Conformational changes in the reaction of pyridoxal kinase.
Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC
J Biol Chem 279 17459-65 (2004)
PMID: 14722069

Function and Biology Details

Reaction catalysed: 
ATP + pyridoxal = ADP + pyridoxal 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-160609 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal kinase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 312 amino acids
Theoretical weight: 34.86 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: P82197 (Residues: 1-312; Coverage: 100%)
Gene names: PDXK, PKH
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand PLP 8 x PLP
Ligand ADP 8 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P43
Unit cell:
a: 109.088Å b: 109.088Å c: 284.272Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.229 0.281

Quick links

Citations

3 review citations

Mitochondrial function and toxicity: role of B vitamins on the one-carbon transfer pathways.
Depeint et al. (2006)
2 more

1 mention without citation

Purification, crystallization and preliminary X-ray diffraction analysis of pyridoxal kinase from Plasmodium falciparum (PfPdxK).
Kronenberger et al. (2014)