5DLT
Crystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol
- PDB DOI: https://doi.org/10.2210/pdb5DLT/pdb
- Classification: HYDROLASE
- Organism(s): Rattus norvegicus
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2015-09-07 Released: 2016-04-13 
- Funding Organization(s): NWO
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.196 
- R-Value Work: 0.171 
- R-Value Observed: 0.172 
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 | 827 | Rattus norvegicus | Mutation(s): 2  Gene Names: Enpp2, Atx, Npps2 EC: 3.1.4.39 | ||
UniProt | |||||
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610  Go to UniProtKB:  Q64610 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q64610 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
5JK Query on 5JK | E [auth A] | 7alpha-hydroxycholesterol C27 H46 O2 OYXZMSRRJOYLLO-RVOWOUOISA-N | |||
IOD Query on IOD | G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
GOL Query on GOL | CA [auth A] DA [auth A] EA [auth A] FA [auth A] GA [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
SCN Query on SCN | JA [auth A] Q [auth A] R [auth A] S [auth A] T [auth A] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
NA Query on NA | AA [auth A], BA [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TPO Query on TPO | A | L-PEPTIDE LINKING | C4 H10 N O6 P | THR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.196 
- R-Value Work: 0.171 
- R-Value Observed: 0.172 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 53.671 | α = 98.72 |
b = 63.482 | β = 105.8 |
c = 70.715 | γ = 99.97 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |
Coot | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-04-13  Deposition Author(s): Hausmann, J., Joosten, R.P., Perrakis, A.
Funding Organization | Location | Grant Number |
---|---|---|
NWO | Netherlands | 700.10.354 |
NWO | Netherlands | 723.013.003 |
Revision History (Full details and data files)
- Version 1.0: 2016-04-13
Type: Initial release - Version 1.1: 2016-04-27
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary