Crystal structure of bovine milk xanthine dehydrogenase with a covalently bound oxipurinol inhibitor

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Ligands and binding sites

• FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
• MTE · Phosphonic acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl)ester · ligand · 2 copies · chains A, B
• MOW · Oxo(sulfanyl)molybdenum(IV) ION · ligand · 2 copies · chains A, B
• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• 141 · Oxypurinol · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• CO3 · Carbonate ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 7 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3106 Ų buried · 55 hydrogen bonds · protein-protein

Compared structures

• 3BDJ · Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound… · the same entry in another collection · chain A against A, TM-score 1.00
• P80457 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P80457) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P80457
• Elsewhere: RCSB PDB 3BDJ · PDBe 3BDJ · UniProt P80457