5VEM
Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)
- PDB DOI: https://doi.org/10.2210/pdb5VEM/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2017-04-05 Released: 2017-09-20 
- Funding Organization(s): Canadian Institutes of Health Research (CIHR)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.227 
- R-Value Work: 0.196 
- R-Value Observed: 0.197 
wwPDB Validation   3D Report Full Report
This is version 2.0 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 5 | 416 | Homo sapiens | Mutation(s): 0  Gene Names: ENPP5, UNQ550/PRO1107 EC: 3.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UJA9 (Homo sapiens) Explore Q9UJA9  Go to UniProtKB:  Q9UJA9 | |||||
PHAROS:  Q9UJA9 GTEx:  ENSG00000112796  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9UJA9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | L [auth A] M [auth A] N [auth A] R [auth B] S [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] K [auth A] O [auth B] P [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.227 
- R-Value Work: 0.196 
- R-Value Observed: 0.197 
- Space Group: P 31
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 109.411 | α = 90 |
b = 109.411 | β = 90 |
c = 134.82 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-09-20  Deposition Author(s): Gorelik, A., Randriamihaja, A., Illes, K., Nagar, B.
Funding Organization | Location | Grant Number |
---|---|---|
Canadian Institutes of Health Research (CIHR) | Canada | MOP-133535 |
Revision History (Full details and data files)
- Version 1.0: 2017-09-20
Type: Initial release - Version 1.1: 2017-09-27
Changes: Author supporting evidence - Version 1.2: 2017-11-22
Changes: 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