› 5ege

X-ray diffraction
2Å resolution

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase

Released:
DOI: 10.2210/pdb5ege/pdb
PDB entry 5ege coloured by chain, front view.
PDB entry 5ege coloured by chain, side view.
PDB entry 5ege coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase.
Morita J, Kano K, Kato K, Takita H, Sakagami H, Yamamoto Y, Mihara E, Ueda H, Sato T, Tokuyama H, Arai H, Asou H, Takagi J, Ishitani R, Nishimasu H, Nureki O, Aoki J
Sci Rep 6 20995 (2016)
PMID: 26888014

Function and Biology Details

Reaction catalysed: 
sn-glycero-3-phosphocholine + H(2)O = glycerol + 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-183861 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Glycerophosphocholine cholinephosphodiesterase ENPP6 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 429 amino acids
Theoretical weight: 49.6 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8BGN3 (Residues: 1-421; Coverage: 96%)
Gene name: Enpp6
Sequence domains: Type I phosphodiesterase / nucleotide pyrophosphatase
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand NAG 7 x NAG
Ligand ZN 8 x ZN
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P1
Unit cell:
a: 64.29Å b: 78.24Å c: 103.64Å
α: 90.04° β: 89.98° γ: 114.61°
R-values:
R R work R free
0.169 0.167 0.206
Expression system: Homo sapiens

Quick links

Citations

9 review citations

Oligodendroglia-lineage cells in brain plasticity, homeostasis and psychiatric disorders.
Birey et al. (2017)
8 more

2 mentions without citation

Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase.
Morita et al. (2016)
1 more