Hif prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to hif-1ALPHA nodd-L397C/D412C and N-oxalylglycine (nog) (complex-2)

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 31% strand (DSSP).

Ligands and binding sites

• OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
• MN · Manganese (II) ion · metal · 2 copies · chains A, C, B, D
• SO4 · Sulfate ion · ion · chains A, C

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–C · 1198 Ų buried · 15 hydrogen bonds · protein-protein
• B–D · 1181 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 595 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 202 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 180 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 5LA9 · HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C… · 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 0.99
• Q16665 · AlphaFold monomer V2.0 prediction for hypoxia-inducible factor 1-alpha (Q16665) · a predicted model of the same protein · chain C against A, TM-score 0.21

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 5LA9 · PDBe 5LA9 · UniProt Q9GZT9 · UniProt Q16665