Crystal structure of xanthine oxidase in complex with lumazine

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).

Ligands and binding sites

• FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, L, N
• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, L, M
• 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, C, L, N
• MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains C, N
• LUZ · pteridine-2,4(1H,3H)-dione · ligand · 2 copies · chains C, N
• CA · Calcium ion · metal · chains C

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

9 interfaces between chains.

• C–N · 2981 Ų buried · 58 hydrogen bonds · protein-protein
• A–C · 2125 Ų buried · 38 hydrogen bonds · protein-protein
• L–N · 2111 Ų buried · 34 hydrogen bonds · protein-protein
• B–C · 1452 Ų buried · 17 hydrogen bonds · protein-protein
• L–M · 1314 Ų buried · 15 hydrogen bonds · protein-protein

Compared structures

• 3ETR · Crystal structure of xanthine oxidase in complex with lumazine · the same entry in another collection · chain N against N, TM-score 1.00
• P80457 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P80457) · a predicted model of the same protein · chain N against A, TM-score 1.00

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 3ETR · PDBe 3ETR · UniProt P80457