5DLW

Crystal structure of Autotaxin (ENPP2) with tauroursodeoxycholic acid (TUDCA) and lysophosphatidic acid (LPA)

PDB DOI: https://doi.org/10.2210/pdb5DLW/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-09-07 Released: 2016-04-13
Deposition Author(s): Keune, W.J., Heidebrecht, T., Joosten, R.P., Perrakis, A.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216
R-Value Work: 0.188
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 99.34 kDa
Atom Count: 6,809
Modelled Residue Count: 781
Deposited Residue Count: 827
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2	A	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 Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G91845HM GlyCosmos: G91845HM GlyGen: G91845HM

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5D5 Query on 5D5 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	2-{[(3alpha,5beta,7alpha,8alpha,14beta,17alpha)-3,7-dihydroxy-24-oxocholan-24-yl]amino}ethanesulfonic acid C₂₆ H₄₅ N O₆ S BHTRKEVKTKCXOH-LBSADWJPSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NKP Query on NKP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C₂₁ H₄₁ O₇ P WRGQSWVCFNIUNZ-SQUSKLHYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], 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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	Y [auth A], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain Y [auth A] Focus chain Z [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A]	W [auth A], X [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5D5	Binding MOAD: 5DLW	Ki: 9000 (nM) from 1 assay(s)
5D5	BindingDB: 5DLW	IC50: 1.03e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216
R-Value Work: 0.188
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.197	α = 90
b = 93.051	β = 90
c = 149.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

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