Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate

Structure

x-ray diffraction · resolution 2.3 · 2 distinct chains · 34% 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 · 6 copies · chains A, B, C, D, F, E
• PO4 · Phosphate ion · ion · 12 copies · chains A, C, B, D, E, F

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

Pockets

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

Interfaces

7 interfaces between chains.

• E–F · 1471 Ų buried · 17 hydrogen bonds · protein-protein
• D–F · 1468 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 1460 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 1447 Ų buried · 18 hydrogen bonds · protein-protein
• D–E · 1418 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

• 5ETJ · Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human… · the same entry in another collection · chain F against F, TM-score 1.00
• P00491 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P00491) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P00491
• Elsewhere: RCSB PDB 5ETJ · PDBe 5ETJ · UniProt P00491