Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalyl glycine (nog), hif-1ALPHA codd (556-574) and a rapid-derived cyclic peptide 3C (14-mer)

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 30% strand (DSSP).

Ligands and binding sites

• 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains A, B
• OGA · N-oxalylglycine · ligand · chains A, S
• MN · Manganese (II) ion · metal · chains A, S
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–S · 1134 Ų buried · 16 hydrogen bonds · protein-protein
• A–B · 802 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 d-amino (covalent ligand, D-amino acid).

Compared structures

• 6YW3 · HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9GZT9 · AlphaFold monomer V2.0 prediction for egl nine homolog 1 (Q9GZT9) · a predicted model of the same protein · chain A against A, TM-score 0.97
• Q16665 · AlphaFold monomer V2.0 prediction for hypoxia-inducible factor 1-alpha (Q16665) · a predicted model of the same protein · chain S against A, TM-score 0.41

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9GZT9
• Every structure of UniProt Q16665
• Elsewhere: RCSB PDB 6YW3 · PDBe 6YW3 · UniProt Q9GZT9 · UniProt Q16665