Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-PYRROLO[3,2- D]PYRIMIDIN-7-YL)METHYL)-4-((prop-2-yn-1-YLTHIO)METHYL)PYRROLIDIN-3- ol

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).

Ligands and binding sites

• OS2 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-{[(prop-2-yn-1-yl) sulfanyl]methyl}pyrrolidin-3-ol · ligand · chains A
• CL · Chloride ion · ion · 2 copies · chains A
• PO4 · Phosphate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

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

Compared structures

• 6DYZ · Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q13126 · AlphaFold monomer V2.0 prediction for S-methyl-5'-thioadenosine phosphorylase (Q13126) · 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 Q13126
• Elsewhere: RCSB PDB 6DYZ · PDBe 6DYZ · UniProt Q13126