3WAY

Crystal Structure of Autotaxin in Complex with 4BoA

• PDB DOI: https://doi.org/10.2210/pdb3WAY/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-05-09 Released: 2013-07-31 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.31 kDa 
• Atom Count: 7,011 
• Modelled Residue Count: 787 
• Deposited Residue Count: 831 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	831	Mus musculus	Mutation(s): 0  Gene Names: Enpp2 EC: 3.1.4.39
UniProt
Find proteins for Q9R1E6 (Mus musculus) Explore Q9R1E6  Go to UniProtKB:  Q9R1E6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47410OF GlyCosmos:  G47410OF GlyGen:  G47410OF

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DWY	Y [auth A]	[4-({4-[(5Z)-5-(3,4-dichlorobenzylidene)-4-oxo-4,5-dihydro-1,3-thiazol-2-yl]piperazin-1-yl}methyl)phenyl]boronic acid C21 H20 B Cl2 N3 O3 S CKUAZJLGUCZSNN-UNOMPAQXSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	J [auth A], K [auth A], L [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DWY	BindingDB:  3WAY	IC50: 22 (nM) from 1 assay(s)
	PDBBind:  3WAY	IC50: 22 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.221 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.556	α = 90
b = 94.524	β = 93.98
c = 75.242	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary