3WAX
Crystal Structure of Autotaxin in Complex with 3BoA
- PDB DOI: https://doi.org/10.2210/pdb3WAX/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Mus musculus
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2013-05-09 Released: 2013-07-31 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224 
- R-Value Work: 0.178 
- R-Value Observed: 0.180 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 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 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9R1E6 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G16404YH GlyCosmos:  G16404YH GlyGen:  G16404YH |
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
DWX Query on DWX | CA [auth A] | [3-({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 ZCKGWOBAJNWRNC-UNOMPAQXSA-N | |||
ZN Query on ZN | E [auth A], F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
EDO Query on EDO | AA [auth A] BA [auth A] L [auth A] M [auth A] N [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
SCN Query on SCN | J [auth A], K [auth A] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | G [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
K Query on K | I [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
NA Query on NA | H [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224 
- R-Value Work: 0.178 
- R-Value Observed: 0.180 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.607 | α = 90 |
b = 94.479 | β = 93.9 |
c = 75.305 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2013-07-31  Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.
Revision History (Full details and data files)
- 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