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X-ray diffraction
2.15Å resolution

Crystal structure of human phytanoyl-COA dioxygenase phyhd1 2-oxoglutarate and iron complex

Released:
DOI: 10.2210/pdb3obz/pdb
PDB entry 3obz coloured by chain, front view.
PDB entry 3obz coloured by chain, side view.
PDB entry 3obz coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zhang Z, McDonough MA, Schofield CJ

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178276 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phytanoyl-CoA dioxygenase domain-containing protein 1 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 32.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SRE7 (Residues: 1-291; Coverage: 100%)
Gene name: PHYHD1
Sequence domains: Phytanoyl-CoA dioxygenase (PhyH)
Structure domains: q2cbj1_9rhob like domain

Ligands and Environments

2 bound ligands:
Ligand AKG 1 x AKG
Ligand FE2 1 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OXFORD DIFFRACTION SUPERNOVA
Spacegroup: P3121
Unit cell:
a: 92.366Å b: 92.366Å c: 81.754Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.233 0.233 0.274
Expression system: Escherichia coli BL21(DE3)

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