› 5tcd

X-ray diffraction
2.4Å resolution

Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine

Released:
DOI: 10.2210/pdb5tcd/pdb
PDB entry 5tcd coloured by chain, front view.
PDB entry 5tcd coloured by chain, side view.
PDB entry 5tcd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the human alkaline sphingomyelinase provides insights into substrate recognition.
Gorelik A, Liu F, Illes K, Nagar B
J Biol Chem 292 7087-7094 (2017)
PMID: 28292932

Function and Biology Details

Reaction catalysed: 
Sphingomyelin + H(2)O = N-acylsphingosine + phosphocholine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180421 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Ectonucleotide pyrophosphatase/phosphodiesterase family member 7 Chain: A
Molecule details ›
Chain: A
Length: 422 amino acids
Theoretical weight: 48.38 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q6UWV6 (Residues: 17-433; Coverage: 93%)
Gene names: ENPP7, UNQ3077/PRO9912
Sequence domains: Type I phosphodiesterase / nucleotide pyrophosphatase
Structure domains: Alkaline Phosphatase, subunit A

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
5 bound ligands:
Ligand ZN 2 x ZN
Ligand NAG 1 x NAG
Ligand NA 1 x NA
Ligand IOD 37 x IOD
Ligand PC 1 x PC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P3121
Unit cell:
a: 104.223Å b: 104.223Å c: 113.893Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.173 0.208
Expression system: Spodoptera frugiperda

Quick links

Citations

6 review citations

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

5 mentions without citation

Structure and function of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family: Tidying up diversity.
Borza et al. (2022)
4 more