Purine nucleoside phosphorylase from E. COLI in complex with formycin a derivative and phosphate

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 30% strand (DSSP).

Ligands and binding sites

• FM2 · 2-(7-amino-6-methyl-3H-pyrazolo[4,3-d]pyrimidin-3-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · 3 copies · chains A, D, B, E, C, F
• FM1 · 2-hydroxymethyl-5-(7-methylamino-3H-pyrazolo[4,3-d]pyrimidin-3-yl)-tetrahydro-furan-3,4-diol · ligand · 3 copies · chains A, D, B, E, C, F
• PO4 · Phosphate ion · ion · 6 copies · chains A, D, B, E, C, F

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

Pockets

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

Interfaces

12 interfaces between chains.

• C–F · 1774 Ų buried · 2 hydrogen bonds · protein-protein
• C–E · 1765 Ų buried · 25 hydrogen bonds · protein-protein
• A–D · 1758 Ų buried · 2 hydrogen bonds · protein-protein
• B–E · 1757 Ų buried · 2 hydrogen bonds · protein-protein
• B–D · 1756 Ų buried · 23 hydrogen bonds · protein-protein

Compared structures

• 1K9S · Purine nucleoside phosphorylase from E. COLI in complex with formycin a derivative and… · the same entry in another collection · chain F against F, TM-score 1.00
• P0ABP8 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP8) · a predicted model of the same protein · chain C 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 P0ABP8
• Elsewhere: RCSB PDB 1K9S · PDBe 1K9S · UniProt P0ABP8