› 3rom

X-ray diffraction
2.04Å resolution

Crystal structure of human CD38 in complex with compound CZ-48

Released:
DOI: 10.2210/pdb3rom/pdb
PDB entry 3rom coloured by chain, front view.
PDB entry 3rom coloured by chain, side view.
PDB entry 3rom coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Catalysis-based inhibitors of the calcium signaling function of CD38.
Kwong AK, Chen Z, Zhang H, Leung FP, Lam CM, Ting KY, Zhang L, Hao Q, Zhang LH, Lee HC
Biochemistry 51 555-64 (2012)
PMID: 22142305

Function and Biology Details

Reactions catalysed: 
(1a) NADP(+) = 2'-phospho-cyclic ADP-ribose + nicotinamide
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151306 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 254 amino acids
Theoretical weight: 29.54 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P28907 (Residues: 45-296; Coverage: 84%)
Gene name: CD38
Sequence domains: ADP-ribosyl cyclase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 48Z 2 x 48Z
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 41.914Å b: 50.847Å c: 68.617Å
α: 65.21° β: 83.6° γ: 82.52°
R-values:
R R work R free
0.185 0.183 0.227
Expression system: Komagataella pastoris

Quick links

Citations

7 review citations

The Multi-faceted Ecto-enzyme CD38: Roles in Immunomodulation, Cancer, Aging, and Metabolic Diseases.
Hogan et al. (2019)
6 more

1 mention without citation

Resolving the topological enigma in Ca2+ signaling by cyclic ADP-ribose and NAADP.
Lee et al. (2019)