5B22 | pdb_00005b22

Dimer structure of murine Nectin-3 D1D2

• PDB DOI: https://doi.org/10.2210/pdb5B22/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-12-28 Released: 2016-12-28 
• Deposition Author(s): Takebe, K., Sangawa, T., Katsutani, T., Narita, H., Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Dimer structure of murine Nectin-3 D1D2

Sangawa, T., Takebe, K., Katsutani, T., Narita, H., Suzuki, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.43 kDa 
• Atom Count: 3,522 
• Modeled Residue Count: 420 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nectin-3	A, B	211	Mus musculus	Mutation(s): 0  Gene Names: Nectin3, Pvrl3
UniProt
Find proteins for Q9JLB9 (Mus musculus) Explore Q9JLB9  Go to UniProtKB:  Q9JLB9
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9JLB9-1

Oligosaccharides

Help

Entity ID: 2
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	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.65	α = 90
b = 72.88	β = 116.36
c = 81.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Takebe, K., Sangawa, T., Katsutani, T., Narita, H., Suzuki, M.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: 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: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary