PDBe 6h00

X-ray diffraction
1.66Å resolution

Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant

Released:
Source organism: Homo sapiens
Entry authors: Mackinnon S, Wilson MP, Shrestha L, Bezerra GA, Newman J, Fox N, Sorrell F, Arrowsmith CH, Edwards A, Bountra C, Clayton PT, Mills PB, Yue WW

Function and Biology Details

Reaction catalysed:
Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2)
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxine-5'-phosphate oxidase Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NVS9 (Residues: 1-261; Coverage: 100%)
  • Best match: Q9NVS9-2 (Residues: 1-46)
Gene name: PNPO
Sequence domains:

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P3121
Unit cell:
a: 83.33Å b: 83.33Å c: 58.93Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.169 0.203
Expression system: Escherichia coli