4B56
Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)
- PDB DOI: https://doi.org/10.2210/pdb4B56/pdb
- Classification: HYDROLASE
- Organism(s): Mus musculus
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2012-08-02 Released: 2012-09-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.234 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
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 1 | 820 | Mus musculus | Mutation(s): 0  EC: 3.1.4.1 (PDB Primary Data), 3.6.1.9 (PDB Primary Data) | ||
UniProt | |||||
Find proteins for P06802 (Mus musculus) Explore P06802  Go to UniProtKB:  P06802 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06802 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
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 | C, E | 5 | N-Glycosylation | ||
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 | K [auth A], L [auth A], Q [auth B], R [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PO4 Query on PO4 | J [auth A], P [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
ZN Query on ZN | G [auth A], H [auth A], M [auth B], N [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | I [auth A], O [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.234 
- R-Value Work: 0.200 
- R-Value Observed: 0.202 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 103.385 | α = 90 |
b = 105.412 | β = 90 |
c = 245.258 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2012-09-19  Deposition Author(s): Jansen, S., Perrakis, A., Ulens, C., Winkler, C., Andries, M., Joosten, R.P., Van Acker, M., Luyten, F.P., Moolenaar, W.H., Bollen, M.
Revision History (Full details and data files)
- Version 1.0: 2012-09-19
Type: Initial release - Version 1.1: 2012-10-17
Changes: Database references - Version 1.2: 2012-11-21
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary