6C01

Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c)

PDB DOI: https://doi.org/10.2210/pdb6C01/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-12-27 Released: 2018-05-02
Deposition Author(s): Gorelik, A., Randriamihaja, A., Illes, K., Nagar, B.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 203.61 kDa
Atom Count: 14,750
Modelled Residue Count: 1,626
Deposited Residue Count: 1,676
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 3	A, B	838	Homo sapiens	Mutation(s): 0 Gene Names: ENPP3, PDNP3 EC: 3.1.4.1 (PDB Primary Data), 3.6.1.9 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O14638 (Homo sapiens) Explore O14638 Go to UniProtKB: O14638
PHAROS: O14638 GTEx: ENSG00000154269
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14638
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, K, R	2		N-Glycosylation	Interactions Focus chain C Focus chain K Focus chain R Interactions & Density Focus chain C Focus chain K Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, N	3		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain N Interactions & Density Focus chain D Focus chain F Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, J, M, O E, H, J, M, O, Q	3		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain J Focus chain M Focus chain O Focus chain Q Interactions & Density Focus chain E Focus chain H Focus chain J Focus chain M Focus chain O Focus chain Q
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	I	4		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	P	5		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain V [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain V [auth A]	AA [auth B], V [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain V [auth A] Interactions & Density Focus chain AA [auth B] Focus chain V [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	S [auth A], T [auth A], X [auth B], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain Z [auth B] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B]	U [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain Z [auth B] Interactions & Density Focus chain U [auth A] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain BA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain BA [auth B]	BA [auth B], W [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain W [auth A] Interactions & Density Focus chain BA [auth B] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.184	α = 90
b = 133.64	β = 90
c = 167.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-133535

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2018-06-13
Changes: Data collection, Database references
Version 1.2: 2018-07-18
Changes: Data collection, Database references
Version 1.3: 2020-01-08
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary