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

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 33% 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
• MN · Manganese (II) ion · metal · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

1 interface between chains.

• A–B · 766 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6YW4 · HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a… · 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 0.98

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
• Elsewhere: RCSB PDB 6YW4 · PDBe 6YW4 · UniProt Q9GZT9