› 6h00

X-ray diffraction
1.66Å resolution

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

Released:
DOI: 10.2210/pdb6h00/pdb
PDB entry 6h00 coloured by chain, front view.
PDB entry 6h00 coloured by chain, side view.
PDB entry 6h00 coloured by chain, top view.
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)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192639 (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%)
Gene name: PNPO
Sequence domains:
Structure domains: Electron Transport, Fmn-binding Protein; Chain A

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:
Ligand SO4 3 x SO4
Ligand EDO 4 x EDO
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

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