› 5uvg

X-ray diffraction
1.85Å resolution

Crystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with insertion deleted and calcium bound

Released:
DOI: 10.2210/pdb5uvg/pdb
PDB entry 5uvg coloured by chain, front view.
PDB entry 5uvg coloured by chain, side view.
PDB entry 5uvg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation.
Airola MV, Shanbhogue P, Shamseddine AA, Guja KE, Senkal CE, Maini R, Bartke N, Wu BX, Obeid LM, Garcia-Diaz M, Hannun YA
Proc Natl Acad Sci U S A 114 E5549-E5558 (2017)
PMID: 28652336

Function and Biology Details

Reaction catalysed: 
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-192694 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingomyelin phosphodiesterase 3 Chain: A
Molecule details ›
Chain: A
Length: 371 amino acids
Theoretical weight: 41.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NY59 (Residues: 117-651; Coverage: 57%)
Gene name: SMPD3
Sequence domains: Endonuclease/Exonuclease/phosphatase family

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 73.61Å b: 91.05Å c: 50.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.162 0.197
Expression system: Escherichia coli

Quick links

Citations

18 review citations

Sphingolipid metabolism in cancer signalling and therapy.
Ogretmen B. (2018)
17 more

9 mentions without citation

Small Molecule Inhibitors Targeting Biosynthesis of Ceramide, the Central Hub of the Sphingolipid Network.
Skácel et al. (2021)
8 more