Crystal structure of human CD38 in complex with 4'-thioribose NAD+

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).

Ligands and binding sites

• ZNA · [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B

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 · 338 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

• 6EDR · Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+ · the same entry in another collection · chain A against A, TM-score 1.00
• P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P28907
• Elsewhere: RCSB PDB 6EDR · PDBe 6EDR · UniProt P28907