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-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl) PROPYL)THIO)METHYL)PYRROLIDIN-3-ol

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).

Ligands and binding sites

• OS5 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl) propyl]sulfanyl}methyl)pyrrolidin-3-ol · ligand · 3 copies · chains A, C, B
• CL · Chloride ion · ion · 4 copies · chains A, B, C
• EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
• ACY · Acetic acid · additive · chains A, B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–B · 1115 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 1090 Ų buried · 13 hydrogen bonds · protein-protein
• B–C · 1083 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 6DZ2 · 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 0.97

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 6DZ2 · PDBe 6DZ2 · UniProt Q13126