› 5fib

X-ray diffraction
2.8Å resolution

Open form of murine Acid Sphingomyelinase

Released:
DOI: 10.2210/pdb5fib/pdb
Model geometry
Fit model/data
PDB entry 5fib coloured by chain, front view.
PDB entry 5fib coloured by chain, side view.
PDB entry 5fib 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
OpenAccess logo 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 (7 distinct):
Sphingomyelin phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
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, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand ZN 6 x ZN
Ligand SO4 17 x SO4
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P4212
Unit cell:
a: 181.173Å b: 181.173Å c: 109.891Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.238
Expression system: Spodoptera frugiperda

Quick links

Citations

23 review citations

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

3 mentions without citation

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