3NKM
Crystal structure of mouse autotaxin
- PDB DOI: https://doi.org/10.2210/pdb3NKM/pdb
- Classification: HYDROLASE
- Organism(s): Mus musculus
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2010-06-20 Released: 2011-01-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.163 
- R-Value Observed: 0.166 
This is version 2.0 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, Npps2, Pdnp2 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)-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 8 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NKP Query on NKP | K [auth A] | (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C21 H41 O7 P WRGQSWVCFNIUNZ-SQUSKLHYSA-N | |||
SO4 Query on SO4 | J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
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] CA [auth A] DA [auth A] N [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
SCN Query on SCN | L [auth A], M [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: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.163 
- R-Value Observed: 0.166 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.588 | α = 90 |
b = 94.731 | β = 94.05 |
c = 75.652 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2011-01-19  Deposition Author(s): Nishimasu, H., Ishitani, R., Mihara, E., Takagi, J., Aoki, J., Nureki, O.
Revision History (Full details and data files)
- Version 1.0: 2011-01-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2014-02-19
Changes: Database references - Version 1.3: 2017-11-08
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary