› 5jg8

X-ray diffraction
2.8Å resolution

Crystal structure of human acid sphingomyelinase

Released:
DOI: 10.2210/pdb5jg8/pdb
PDB entry 5jg8 coloured by chain, front view.
PDB entry 5jg8 coloured by chain, side view.
PDB entry 5jg8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.
Xiong ZJ, Huang J, Poda G, Pomès R, Privé GG
J Mol Biol 428 3026-42 (2016)
PMID: 27349982

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148050 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Sphingomyelin phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 586 amino acids
Theoretical weight: 65.32 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
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
3 bound ligands:
Ligand ZN 4 x ZN
Ligand ACT 2 x ACT
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 69.531Å b: 143.658Å c: 193.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.279
Expression system: Homo sapiens

Quick links

Citations

10 review citations

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