Crystal structure of trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-PYRROLO[3,2- D]PYRIMIDIN-7-YL)METHYL]-2-(HYDROXYMETHYL)PYRROLIDIN-3,4-diol

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Ligands and binding sites

• JMQ · 7-(((2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl)methyl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1332 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 3EPW · Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor… · the same entry in another collection · chain A 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 Q9GPQ4
• Elsewhere: RCSB PDB 3EPW · PDBe 3EPW · UniProt Q9GPQ4