Bovine milk xanthine dehydrogenase Y-700 bound form

Structure

x-ray diffraction · 2 distinct chains · 33% 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
• MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains A, B
• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• YSH · 1-[3-cyano-4-(neopentyloxy)phenyl]-1H-pyrazole-4-carboxylic acid · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 4 copies · chains A, B
• GOL · Glycerol · additive · 21 copies · chains A, B
• ACY · Acetic acid · additive · 2 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 · 3099 Ų buried · 56 hydrogen bonds · protein-protein

Compared structures

• 1VDV · Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form · 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 B 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 1VDV · PDBe 1VDV · UniProt P80457