› 5lbb

X-ray diffraction
1.7Å resolution

HIF prolyl hydroxylase 2 (PHD2/EGLN1) R396T variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

Released:
DOI: 10.2210/pdb5lbb/pdb
PDB entry 5lbb coloured by chain, front view.
PDB entry 5lbb coloured by chain, side view.
PDB entry 5lbb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.
Chowdhury R, Leung IK, Tian YM, Abboud MI, Ge W, Domene C, Cantrelle FX, Landrieu I, Hardy AP, Pugh CW, Ratcliffe PJ, Claridge TD, Schofield CJ
Nat Commun 7 12673 (2016)
PMID: 27561929

Function and Biology Details

Reaction catalysed: 
Hypoxia-inducible factor-L-proline + 2-oxoglutarate + O(2) = hypoxia-inducible factor-trans-4-hydroxy-L-proline + succinate + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190451 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Egl nine homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 28.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZT9 (Residues: 181-426; Coverage: 58%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: q2cbj1_9rhob like domain

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand UN9 1 x UN9
Ligand BCT 1 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P63
Unit cell:
a: 110.199Å b: 110.199Å c: 39.717Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.153 0.152 0.178
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

13 review citations

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

2 mentions without citation

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.
Chowdhury et al. (2016)
1 more