› 4nhy

X-ray diffraction
2.6Å resolution

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

Released:
DOI: 10.2210/pdb4nhy/pdb
PDB entry 4nhy coloured by chain, front view.
PDB entry 4nhy coloured by chain, side view.
PDB entry 4nhy 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

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-185400 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl 3-hydroxylase OGFOD1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
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

3 bound ligands:
Ligand MN 4 x MN
Ligand GOL 3 x GOL
Ligand PD2 4 x PD2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21212
Unit cell:
a: 108.68Å b: 130.473Å c: 175.784Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.19 0.226
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

4 mentions without citation

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