› 5b6a

X-ray diffraction
2Å resolution

Structure of Pyridoxal Kinasefrom Pseudomonas Aeruginosa

Released:
DOI: 10.2210/pdb5b6a/pdb
PDB entry 5b6a coloured by chain, front view.
PDB entry 5b6a coloured by chain, side view.
PDB entry 5b6a coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Crystal structure and catalytic mechanism of pyridoxal kinase from Pseudomonas aeruginosa.
Kim MI, Hong M
Biochem Biophys Res Commun 478 300-306 (2016)
PMID: 27425248

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-190914 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal kinase PdxY Chain: A
Molecule details ›
Chain: A
Length: 288 amino acids
Theoretical weight: 31.32 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HT57 (Residues: 1-288; Coverage: 100%)
Gene names: PA5516, pdxY
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand TRS 1 x TRS
Ligand MG 1 x MG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P3121
Unit cell:
a: 102.547Å b: 102.547Å c: 61.492Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.195 0.225
Expression system: Escherichia coli

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Citations

1 mention without citation

Synthesis, spectroscopic investigation, molecular docking and DFT studies of novel (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA).
Devi et al. (2018)