› 3keu

X-ray diffraction
2.1Å resolution

Crystal Structure of Human PL Kinase with bound PLP and ATP

Released:
DOI: 10.2210/pdb3keu/pdb
PDB entry 3keu coloured by chain, front view.
PDB entry 3keu coloured by chain, side view.
PDB entry 3keu coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Safo MK, Gandhi AK, Musayev FN

Function and Biology Details

Reaction catalysed: 
ATP + pyridoxal = ADP + pyridoxal 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-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

6 bound ligands:
Ligand MG 4 x MG
Ligand NA 2 x NA
Ligand ATP 2 x ATP
Ligand PLP 2 x PLP
Ligand MPD 9 x MPD
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: I222
Unit cell:
a: 91.202Å b: 114.585Å c: 169.414Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.209 0.256
Expression system: Escherichia coli

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