› 8j2f

Electron Microscopy
3.07Å resolution

Human neutral shpingomyelinase

Released:
DOI: 10.2210/pdb8j2f/pdb
PDB entry 8j2f coloured by chain, front view.
PDB entry 8j2f coloured by chain, side view.
PDB entry 8j2f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2).
Yi J, Qi B, Yin J, Li R, Chen X, Hu J, Li G, Zhang S, Zhang Y, Yang M
OpenAccess logo Nat Commun 14 7755 (2023)
PMID: 38012235
Related structures: EMD-35948

Function and Biology Details

Reaction catalysed: 
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236251 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingomyelin phosphodiesterase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 423 amino acids
Theoretical weight: 47.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60906 (Residues: 1-423; Coverage: 100%)
Gene name: SMPD2
Sequence domains: Endonuclease/Exonuclease/phosphatase family

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand HP6 2 x HP6
Ligand C14 2 x C14
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.07Å
Relevant EMDB volumes: EMD-35948
Expression system: Homo sapiens

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