6C02

Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c), inactive (T205A), N594S, with alpha,beta-methylene-ATP (AMPCPP)

PDB DOI: https://doi.org/10.2210/pdb6C02/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

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: 1.94 Å
R-Value Free: 0.197
R-Value Work: 0.166
R-Value Observed: 0.168

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: 200.54 kDa
Atom Count: 14,922
Modelled Residue Count: 1,630
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): 2 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, F, J, L, M	2		N-Glycosylation	Interactions Focus chain C Focus chain F Focus chain J Focus chain L Focus chain M Interactions & Density Focus chain C Focus chain F Focus chain J Focus chain L Focus chain M
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, K	3		N-Glycosylation	Interactions Focus chain D Focus chain K Interactions & Density Focus chain D Focus chain K
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, G, N	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain N Interactions & Density Focus chain E Focus chain G Focus chain N
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I	2		N-Glycosylation	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC Query on APC Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain X [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain X [auth A]	EA [auth B], X [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain EA [auth B] Focus chain X [auth A] Interactions & Density Focus chain EA [auth B] Focus chain X [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	CA [auth B], DA [auth B], V [auth A], W [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain V [auth A] Focus chain W [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth B]	O [auth A], P [auth A], Y [auth B], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain Q [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain Q [auth A]	AA [auth B], Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain AA [auth B] Focus chain Q [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	S [auth A], T [auth A], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain R [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain R [auth A]	BA [auth B], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain R [auth A] Interactions & Density Focus chain BA [auth B] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.197
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.656	α = 90
b = 169.457	β = 103.87
c = 79.062	γ = 90

Software Package:

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

Structure Validation

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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: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

6C02

Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c), inactive (T205A), N594S, with alpha,beta-methylene-ATP (AMPCPP)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)