› 3ibq

X-ray diffraction
2Å resolution

Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP

Released:
DOI: 10.2210/pdb3ibq/pdb
PDB entry 3ibq coloured by chain, front view.
PDB entry 3ibq coloured by chain, side view.
PDB entry 3ibq coloured by chain, top view.
Source organism: Lactiplantibacillus plantarum
Entry authors: Bagaria A, Kumaran D, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

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:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-123772 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
pyridoxal kinase Chain: A
Molecule details ›
Chain: A
Length: 282 amino acids
Theoretical weight: 30.41 KDa
Source organism: Lactiplantibacillus plantarum
Expression system: Escherichia coli
UniProt:
  • Canonical: F9UM74 (Residues: 2-272; Coverage: 100%)
Gene names: lp_0863, pdxK
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MG 1 x MG
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2221
Unit cell:
a: 64.357Å b: 69.576Å c: 132.369Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.175 0.219
Expression system: Escherichia coli

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