› 5i81

X-ray diffraction
2.25Å resolution

aSMase with zinc

Released:
DOI: 10.2210/pdb5i81/pdb
PDB entry 5i81 coloured by chain, front view.
PDB entry 5i81 coloured by chain, side view.
PDB entry 5i81 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Zhou YF, Metcalf MC, Garman SC, Edmunds T, Qiu H, Wei RR
Nat Commun 7 13082 (2016)
PMID: 27725636

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

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-148049 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Sphingomyelin phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 583 amino acids
Theoretical weight: 65.11 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P17405 (Residues: 49-631; Coverage: 100%)
Gene names: ASM, SMPD1
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand NAG 6 x NAG
Ligand BMA 1 x BMA
Ligand ZN 2 x ZN
Ligand SO4 11 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6422
Unit cell:
a: 132.629Å b: 132.629Å c: 189.565Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.184 0.205
Expression system: Homo sapiens

Quick links

Citations

4 review citations

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

5 mentions without citation

Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Zhou et al. (2016)
4 more