› 4nhx

X-ray diffraction
2.1Å resolution

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)

Released:
DOI: 10.2210/pdb4nhx/pdb
PDB entry 4nhx coloured by chain, front view.
PDB entry 4nhx coloured by chain, side view.
PDB entry 4nhx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases.
Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA
Structure 23 639-52 (2015)
PMID: 25728928

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185400 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl 3-hydroxylase OGFOD1 Chain: A
Molecule details ›
Chain: A
Length: 562 amino acids
Theoretical weight: 65.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N543 (Residues: 1-542; Coverage: 100%)
Gene names: KIAA1612, OGFOD1, TPA1
Sequence domains:
Structure domains: q2cbj1_9rhob like domain

Ligands and Environments

4 bound ligands:
Ligand MN 1 x MN
Ligand NA 1 x NA
Ligand OGA 1 x OGA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3221
Unit cell:
a: 64.401Å b: 64.401Å c: 232.041Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.189 0.215
Expression system: Escherichia coli

Quick links

Citations

5 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
4 more

5 mentions without citation

Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases.
Horita et al. (2015)
4 more