› 3dzf

X-ray diffraction
2.01Å resolution

Crystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate

Released:
DOI: 10.2210/pdb3dzf/pdb
PDB entry 3dzf coloured by chain, front view.
PDB entry 3dzf coloured by chain, side view.
PDB entry 3dzf 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, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
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

1 bound ligand:
Ligand RF5 6 x RF5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P1
Unit cell:
a: 41.746Å b: 96.156Å c: 103.605Å
α: 79.48° β: 82.72° γ: 86.78°
R-values:
R R work R free
0.205 0.201 0.272
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)