2QVI | pdb_00002qvi

Crystal structure of N-cadherin domains EC12

• PDB DOI: https://doi.org/10.2210/pdb2QVI/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2007-08-08 Released: 2008-08-12 
• Deposition Author(s): Shapiro, L.S., Carroll, K.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.299 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.256 (DCC) 

Literature

Biophysical characterization of N-cadherin and E-cadherin homophilic and heterophilic interactions

Shapiro, L.S., Carroll, K.J., Honig, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.74 kDa 
• Atom Count: 1,765 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-2	A	215	Mus musculus	Mutation(s): 0  Gene Names: Cdh2
UniProt
Find proteins for P15116 (Mus musculus) Explore P15116  Go to UniProtKB:  P15116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.299 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.256 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.657	α = 90
b = 86.902	β = 97.73
c = 46.708	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Shapiro, L.S., Carroll, K.J.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations