› 7g3h

X-ray diffraction
1.64Å resolution

Crystal Structure of rat Autotaxin in complex with [2-[[(2R)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino]pyrimidin-5-yl]-(6-oxa-1-azaspiro[3.3]heptan-1-yl)methanone, i.e. SMILES Clc1ccc2c(c1)C[C@@H](C2)Nc1ncc(cn1)C(=O)N1CCC21COC2 with IC50=0.0678127 microM

Released:
DOI: 10.2210/pdb7g3h/pdb
Model geometry
Fit model/data
PDB entry 7g3h coloured by chain, front view.
PDB entry 7g3h coloured by chain, side view.
PDB entry 7g3h coloured by chain, top view.
Source organism: Rattus norvegicus
Entry authors: Stihle M, Benz J, Hunziker D, Pinard E, Rudolph MG

Function and Biology Details

Reactions catalysed: 
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
A phosphatidylcholine + H(2)O = choline + a phosphatidate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179148 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Autotaxin Chain: A
Molecule details ›
Chain: A
Length: 846 amino acids
Theoretical weight: 97.34 KDa
Source organism: Rattus norvegicus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q64610 (Residues: 28-887; Coverage: 97%)
  • Best match: Q64610-2 (Residues: 28-862)
Gene names: Atx, Enpp2, Npps2
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
7 bound ligands:
Ligand ZN 1 x ZN
Ligand NA 1 x NA
Ligand CA 2 x CA
Ligand CL 1 x CL
Ligand K 1 x K
Ligand ACT 3 x ACT
Ligand XJ6 1 x XJ6
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 83.504Å b: 91.217Å c: 119.043Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.198
Expression system: Homo sapiens

Quick links

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO