Crystal structure of xanthine dehydrogenase (desulfo form) from rhodobacter capsulatus in complex with xanthine

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Ligands and binding sites

• FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, E, G
• 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 · 4 copies · chains A, B, C, D, E, F, G, H
• XAN · Xanthine · ligand · 4 copies · chains B, D, F, H
• MOM · Hydroxy(dioxo)molybdenum · ligand · 4 copies · chains B, D, F, H
• CA · Calcium ion · metal · 4 copies · chains B, D, F, H

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

8 interfaces between chains.

• E–F · 3605 Ų buried · 61 hydrogen bonds · protein-protein
• C–D · 3588 Ų buried · 55 hydrogen bonds · protein-protein
• G–H · 3568 Ų buried · 54 hydrogen bonds · protein-protein
• A–B · 3539 Ų buried · 56 hydrogen bonds · protein-protein
• B–D · 2337 Ų buried · 50 hydrogen bonds · protein-protein

Compared structures

• 2W3S · Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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• Elsewhere: RCSB PDB 2W3S · PDBe 2W3S · UniProt O54050 · UniProt O54051