6F2V
Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with AMP
- PDB DOI: https://doi.org/10.2210/pdb6F2V/pdb
- Classification: HYDROLASE
- Organism(s): Rattus norvegicus
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2017-11-27 Released: 2018-08-01 
- Funding Organization(s): German Research Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.209 
- R-Value Work: 0.194 
- R-Value Observed: 0.194 
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 3 | 749 | Rattus norvegicus | Mutation(s): 3  Gene Names: Enpp3, Pdnp3 EC: 3.1.4.1 (PDB Primary Data), 3.6.1.9 (PDB Primary Data) | ||
UniProt | |||||
Find proteins for P97675 (Rattus norvegicus) Explore P97675  Go to UniProtKB:  P97675 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P97675 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
AMP Query on AMP | H [auth A], N [auth B] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N | |||
NAG Query on NAG | L [auth A], M [auth A], R [auth B], S [auth B], T [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | I [auth A], J [auth A], O [auth B], P [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | K [auth A], Q [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.209 
- R-Value Work: 0.194 
- R-Value Observed: 0.194 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.918 | α = 90 |
b = 125.327 | β = 96.91 |
c = 112.248 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-08-01  Deposition Author(s): Dohler, C., Zebisch, M., Strater, N.
Funding Organization | Location | Grant Number |
---|---|---|
German Research Foundation | Germany | 477/13-2 |
Revision History (Full details and data files)
- Version 1.0: 2018-08-01
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary