› 3dzi

X-ray diffraction
1.73Å resolution

Crystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex

Released:
DOI: 10.2210/pdb3dzi/pdb
PDB entry 3dzi coloured by chain, front view.
PDB entry 3dzi coloured by chain, side view.
PDB entry 3dzi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.
Liu Q, Kriksunov IA, Jiang H, Graeff R, Lin H, Lee HC, Hao Q
Chem Biol 15 1068-78 (2008)
PMID: 18940667

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: 262 amino acids
Theoretical weight: 30.38 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P28907 (Residues: 45-300; Coverage: 85%)
Gene name: CD38
Sequence domains: ADP-ribosyl cyclase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand RGT 1 x RGT
Ligand N 1 x N
Ligand GTP 1 x GTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P1
Unit cell:
a: 41.669Å b: 52.747Å c: 65.133Å
α: 106.09° β: 91.92° γ: 95.27°
R-values:
R R work R free
0.179 0.177 0.211
Expression system: Komagataella pastoris

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Citations

5 review citations

Cyclic ADP-ribose and nicotinic acid adenine dinucleotide phosphate (NAADP) as messengers for calcium mobilization.
Lee HC. (2012)
4 more

1 mention without citation

Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.
Liu et al. (2008)