X-ray structure of human CD38 catalytic domain with 2'-cl-aranad+

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).

Ligands and binding sites

• ROJ · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R})-4-chloranyl-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 2 copies · chains A, B
• PO4 · Phosphate ion · ion · 2 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
• PGE · Triethylene glycol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 555 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 6VUA · X-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+ · 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 B 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 P28907
• Elsewhere: RCSB PDB 6VUA · PDBe 6VUA · UniProt P28907