› 6yw4

X-ray diffraction
1.53Å resolution

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)

Released:
DOI: 10.2210/pdb6yw4/pdb
PDB entry 6yw4 coloured by chain, front view.
PDB entry 6yw4 coloured by chain, side view.
PDB entry 6yw4 coloured by chain, top view.
Source organisms:
Primary publication:
Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Chowdhury R, Abboud MI, McAllister TE, Banerji B, Bhushan B, Sorensen JL, Kawamura A, Schofield CJ
OpenAccess logo Sci Rep 10 21964 (2020)
PMID: 33319810

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167903 (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: 25.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZT9 (Residues: 181-407; Coverage: 53%)
Gene names: C1orf12, EGLN1, PNAS-118, PNAS-137
Sequence domains: 2OG-Fe(II) oxygenase superfamily
PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER) Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.8 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand OGA 1 x OGA
Ligand SO4 2 x SO4
1 modified residue:
Ligand DTY 1 x DTY

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P65
Unit cell:
a: 46.622Å b: 46.622Å c: 203.711Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.162 0.177
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 citations in other articles

Structural Basis of Prolyl Hydroxylase Domain Inhibition by Molidustat.
Figg et al. (2021)