› 8j1k

X-ray diffraction
2.45Å resolution

co-crystal structure of non-carboxylic acid inhibitor with PHD2

Released:
DOI: 10.2210/pdb8j1k/pdb
PDB entry 8j1k coloured by chain, front view.
PDB entry 8j1k coloured by chain, side view.
PDB entry 8j1k coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Xu J, Fu Y, Ding X, Meng Q, Wang L, Zhang M, Ding X, Ren F, Zhavoronkov A

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190450 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Egl nine homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 218 amino acids
Theoretical weight: 24.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GZT9 (Residues: 189-406; Coverage: 51%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily

Ligands and Environments

2 bound ligands:
Ligand SY6 1 x SY6
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P63
Unit cell:
a: 80.843Å b: 80.843Å c: 63.899Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.246 0.242 0.308
Expression system: Escherichia coli

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