Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'- phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Ligands and binding sites

• 9D9 · [5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid · ligand · 3 copies · chains A, B, C
• MG · Magnesium ion · metal · 3 copies · chains A, C
• AZI · Azide ion · ion · chains C

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 1271 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 1251 Ų buried · 15 hydrogen bonds · protein-protein
• A–B · 1215 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 3FUC · Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate… · the same entry in another collection · chain C against C, TM-score 1.00
• P55859 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P55859) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P55859
• Elsewhere: RCSB PDB 3FUC · PDBe 3FUC · UniProt P55859