SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket

Structure

x-ray diffraction · resolution 2.3 · 2 distinct chains · 52% helix, 13% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · 12 copies · chains A, B, C, D
• HFD · 2-fluoro-9-{5-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine · ligand · 4 copies · chains A, B, C, D
• GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
• DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
• NA · Sodium ion · metal · 23 copies · chains A, D, C, B
• MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
• PO4 · Phosphate ion · ion · chains D
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–C · 2167 Ų buried · 30 hydrogen bonds · protein-protein
• B–D · 2137 Ų buried · 27 hydrogen bonds · protein-protein
• A–D · 1932 Ų buried · 19 hydrogen bonds · protein-protein
• B–C · 1924 Ų buried · 20 hydrogen bonds · protein-protein
• A–B · 494 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6DWK · SAMHD1 bound to fludarabine-tp in the catalytic pocket · the same entry in another collection · chain D against D, TM-score 1.00
• Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain B 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 Q9Y3Z3
• Elsewhere: RCSB PDB 6DWK · PDBe 6DWK · UniProt Q9Y3Z3