› 5fic

X-ray diffraction
2.8Å resolution

Open form of murine Acid Sphingomyelinase in presence of lipid

Released:
DOI: 10.2210/pdb5fic/pdb
PDB entry 5fic coloured by chain, front view.
PDB entry 5fic coloured by chain, side view.
PDB entry 5fic coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structure of mammalian acid sphingomyelinase.
Gorelik A, Illes K, Heinz LX, Superti-Furga G, Nagar B
Nat Commun 7 12196 (2016)
PMID: 27435900

Function and Biology Details

Reactions catalysed: 
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
A phosphatidylcholine + H(2)O = 1,2-diacyl-sn-glycerol + phosphocholine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170034 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Sphingomyelin phosphodiesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 538 amino acids
Theoretical weight: 60.43 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q04519 (Residues: 84-611; Coverage: 91%)
Gene names: Asm, Smpd1
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
5 bound ligands:
Ligand ZN 8 x ZN
Ligand PO4 7 x PO4
Ligand CL 5 x CL
Ligand 6E0 2 x 6E0
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P41
Unit cell:
a: 101.75Å b: 101.75Å c: 401.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.236
Expression system: Spodoptera frugiperda

Quick links

Citations

24 review citations

Sphingolipids and their metabolism in physiology and disease.
Hannun et al. (2018)
23 more

1 mention without citation

Crystal structure of mammalian acid sphingomyelinase.
Gorelik et al. (2016)