› 3wax

X-ray diffraction
1.9Å resolution

Crystal Structure of Autotaxin in Complex with 3BoA

Released:
DOI: 10.2210/pdb3wax/pdb
PDB entry 3wax coloured by chain, front view.
PDB entry 3wax coloured by chain, side view.
PDB entry 3wax coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Screening and X-ray crystal structure-based optimization of autotaxin (ENPP2) inhibitors, using a newly developed fluorescence probe.
Kawaguchi M, Okabe T, Okudaira S, Nishimasu H, Ishitani R, Kojima H, Nureki O, Aoki J, Nagano T
ACS Chem Biol 8 1713-21 (2013)
PMID: 23688339

Function and Biology Details

Reaction catalysed: 
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 Chain: A
Molecule details ›
Chain: A
Length: 831 amino acids
Theoretical weight: 95.76 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9R1E6 (Residues: 36-862; Coverage: 99%)
Gene names: Enpp2, Npps2, Pdnp2
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
7 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 1 x CA
Ligand NA 1 x NA
Ligand K 1 x K
Ligand SCN 2 x SCN
Ligand EDO 17 x EDO
Ligand DWX 1 x DWX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P21
Unit cell:
a: 61.607Å b: 94.479Å c: 75.305Å
α: 90° β: 93.9° γ: 90°
R-values:
R R work R free
0.18 0.178 0.224
Expression system: Homo sapiens

Quick links

Citations

14 review citations

Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes.
Ni et al. (2017)
13 more

3 mentions without citation

The Structural Binding Mode of the Four Autotaxin Inhibitor Types that Differentially Affect Catalytic and Non-Catalytic Functions.
Salgado-Polo et al. (2019)
2 more