› 4gtw

X-ray diffraction
2.7Å resolution

Crystal structure of mouse Enpp1 in complex with AMP

Released:
DOI: 10.2210/pdb4gtw/pdb
PDB entry 4gtw coloured by chain, front view.
PDB entry 4gtw coloured by chain, side view.
PDB entry 4gtw coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Kato K, Nishimasu H, Okudaira S, Mihara E, Ishitani R, Takagi J, Aoki J, Nureki O
Proc Natl Acad Sci U S A 109 16876-81 (2012)
PMID: 23027977

Function and Biology Details

Reactions catalysed: 
Hydrolytically removes 5'-nucleotides successively from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139235 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Ectonucleotide pyrophosphatase/phosphodiesterase family member 1, secreted form; Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 823 amino acids
Theoretical weight: 95.12 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9R1E6 (Residues: 51-64; Coverage: 2%)
  • Canonical: P06802 (Residues: 97-906; Coverage: 89%)
Gene names: Enpp1, Enpp2, Npps, Npps2, Pc1, Pdnp1, Pdnp2
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand NAG 4 x NAG
Ligand AMP 2 x AMP
Ligand ZN 4 x ZN
Ligand CA 2 x CA
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P31
Unit cell:
a: 105.283Å b: 105.283Å c: 173.685Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.233 0.231 0.276
Expression system: Homo sapiens

Quick links

Citations

24 review citations

Small molecules targeting the innate immune cGAS‒STING‒TBK1 signaling pathway.
Ding et al. (2020)
23 more

19 mentions without citation

Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Kato et al. (2012)
18 more