Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in complex with dadme-immg

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 30% strand (DSSP).

Ligands and binding sites

• IM5 · 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 6 copies · chains A, B, C, D, E, F
• K · Potassium ion · metal · 3 copies · chains A, B, C, D, E, F
• PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• C–D · 2208 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 2202 Ų buried · 19 hydrogen bonds · protein-protein
• E–F · 2173 Ų buried · 20 hydrogen bonds · protein-protein
• B–C · 1263 Ų buried · 16 hydrogen bonds · protein-protein
• D–E · 1263 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 3PHC · Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex… · the same entry in another collection · chain C against C, TM-score 1.00
• Q8T9Z7 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (Q8T9Z7) · a predicted model of the same protein · 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 Q8T9Z7
• Elsewhere: RCSB PDB 3PHC · PDBe 3PHC · UniProt Q8T9Z7