Crystal structure of HSNUDT16 in complex with diadpr (soaked)

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).

Ligands and binding sites

• C7G · [(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S}, 5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1320 Ų buried · 13 hydrogen bonds · protein-protein

Compared structures

• 6B09 · Crystal structure of HsNUDT16 in complex with diADPR (soaked) · the same entry in another collection · chain A against A, TM-score 1.00
• Q96DE0 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q96DE0) · a predicted model of the same protein · chain B 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 Q96DE0
• Elsewhere: RCSB PDB 6B09 · PDBe 6B09 · UniProt Q96DE0