Crystal structure of xanthine dehydrogenase from rhodobacter capsulatus in complex with bound inhibitor pterin-6-aldehyde

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 25% 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
• XAX · {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum · ligand · 4 copies · chains A, B, C, D, E, F, G, H
• HHR · 6-hydroxymethylpterin · ligand · 4 copies · chains B, D, F, H
• BA · Barium 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 · 3626 Ų buried · 60 hydrogen bonds · protein-protein
• G–H · 3622 Ų buried · 62 hydrogen bonds · protein-protein
• A–B · 3602 Ų buried · 61 hydrogen bonds · protein-protein
• C–D · 3597 Ų buried · 51 hydrogen bonds · protein-protein
• F–H · 2346 Ų buried · 51 hydrogen bonds · protein-protein

Compared structures

• 2W54 · Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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• Elsewhere: RCSB PDB 2W54 · PDBe 2W54 · UniProt O54050 · UniProt O54051