› 2yxu

X-ray diffraction
2.2Å resolution

Human Pyridoxal Kinase

Released:
DOI: 10.2210/pdb2yxu/pdb
PDB entry 2yxu coloured by chain, front view.
PDB entry 2yxu coloured by chain, side view.
PDB entry 2yxu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK
Protein Sci 16 2184-94 (2007)
PMID: 17766369

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-126391 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 312 amino acids
Theoretical weight: 35.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00764 (Residues: 1-312; Coverage: 100%)
Gene names: C21orf124, C21orf97, PDXK, PKH, PNK, PRED79
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

5 bound ligands:
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand PO4 5 x PO4
Ligand ATP 2 x ATP
Ligand MPD 12 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: I222
Unit cell:
a: 90.462Å b: 115.119Å c: 170.201Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.192 0.243
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Vitamin B6: a long known compound of surprising complexity.
Mooney et al. (2009)
2 more

4 mentions without citation

Predicting new indications for approved drugs using a proteochemometric method.
Dakshanamurthy et al. (2012)
3 more