5EGE

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase

PDB DOI: https://doi.org/10.2210/pdb5EGE/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-10-27 Released: 2016-03-09
Deposition Author(s): Morita, J., Kano, K., Kato, K., Takita, H., Ishitani, R., Nishimasu, H., Nureki, O., Aoki, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.167
R-Value Observed: 0.169

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: 204.82 kDa
Atom Count: 15,249
Modelled Residue Count: 1,568
Deposited Residue Count: 1,716
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 6	A, B, C, D	429	Mus musculus	Mutation(s): 2 Gene Names: Enpp6 EC: 3.1.4 (PDB Primary Data), 3.1.4.38 (PDB Primary Data)
UniProt
Find proteins for Q8BGN3 (Mus musculus) Explore Q8BGN3 Go to UniProtKB: Q8BGN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8BGN3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, K	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, L	2		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	DA [auth D] M [auth A] N [auth A] S [auth B] T [auth B] DA [auth D], M [auth A], N [auth A], S [auth B], T [auth B], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C]	AA [auth C] EA [auth D] FA [auth D] O [auth A] P [auth A] AA [auth C], EA [auth D], FA [auth D], O [auth A], P [auth A], U [auth B], V [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain GA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B]	BA [auth C] CA [auth C] GA [auth D] Q [auth A] R [auth A] BA [auth C], CA [auth C], GA [auth D], Q [auth A], R [auth A], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.29	α = 90.04
b = 78.24	β = 89.98
c = 103.64	γ = 114.61

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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Help and Resources

5EGE

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources