› 4tmf

X-ray diffraction
2.05Å resolution

Crystal structure of human CD38 in complex with hydrolysed compound JMS713

Released:
DOI: 10.2210/pdb4tmf/pdb
PDB entry 4tmf coloured by chain, front view.
PDB entry 4tmf coloured by chain, side view.
PDB entry 4tmf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cyclic adenosine 5'-diphosphate ribose analogs without a "southern" ribose inhibit ADP-ribosyl cyclase-hydrolase CD38.
Swarbrick JM, Graeff R, Zhang H, Thomas MP, Hao Q, Potter BV
J Med Chem 57 8517-29 (2014)
PMID: 25226087

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: 257 amino acids
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P28907 (Residues: 50-300; Coverage: 84%)
Gene name: CD38
Sequence domains: ADP-ribosyl cyclase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand JS2 2 x JS2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 41.69Å b: 54.128Å c: 63.319Å
α: 108.58° β: 90.98° γ: 93.98°
R-values:
R R work R free
0.2 0.198 0.227
Expression system: Komagataella pastoris

Quick links

Citations

3 review citations

Modulating NAD+ metabolism, from bench to bedside.
Katsyuba et al. (2017)
2 more

4 mentions without citation

Assessing Molecular Docking Tools to Guide Targeted Drug Discovery of CD38 Inhibitors.
Boittier et al. (2020)
3 more