Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent enzyme-substrate complex.

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).

Ligands and binding sites

• 2NF · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(3-carbamoylpyridin-1-ium-1yl)- 3-fluoro-,4- hydroxyoxolan-2-yl]methyl phosphate · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 951 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

• 3KOU · Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally… · the same entry in another collection · chain A 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 Q9TTF5
• Elsewhere: RCSB PDB 3KOU · PDBe 3KOU · UniProt Q9TTF5