› 8q6d

X-ray diffraction
1.4Å resolution

Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG)

Released:
DOI: 10.2210/pdb8q6d/pdb
PDB entry 8q6d coloured by chain, front view.
PDB entry 8q6d coloured by chain, side view.
PDB entry 8q6d coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Fiorini G, Figg Jr WD, Schofield CJ

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189273 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Egl nine homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 26.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q9GZT9 (Residues: 181-407; Coverage: 53%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Endothelial PAS domain-containing protein 1 Chain: B
Molecule details ›
Chain: B
Length: 20 amino acids
Theoretical weight: 2.31 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q99814 (Residues: 523-542; Coverage: 2%)
Gene names: BHLHE73, EPAS1, HIF2A, MOP2, PASD2
Sequence domains: Hypoxia-inducible factor-1

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Unit cell:
a: 38.07Å b: 42.63Å c: 130.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.167 0.19
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

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