Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with dadme-immg and phosphate

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 23% 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 · 3 copies · chains A, C, B
• PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
• EDO · 1,2-ethanediol · additive · 2 copies · chains B, A, C

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 1484 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 1477 Ų buried · 20 hydrogen bonds · protein-protein
• A–C · 1334 Ų buried · 19 hydrogen bonds · protein-protein

Compared structures

• 4EB8 · Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant… · the same entry in another collection · chain A against A, TM-score 1.00

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• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P00491
• Elsewhere: RCSB PDB 4EB8 · PDBe 4EB8 · UniProt P00491