4HZA | pdb_00004hza

Crystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form

• PDB DOI: https://doi.org/10.2210/pdb4HZA/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-14 Released: 2013-01-30 
• Deposition Author(s): Ramagopal, U.A., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form

Ramagopal, U.A., Samanta, D., Nathenson, S.G., Almo, S.C.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.9 kDa 
• Atom Count: 2,128 
• Modeled Residue Count: 248 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 2	A, B	128	Homo sapiens	Mutation(s): 0  Gene Names: HVEB, PRR2, PVRL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92692 (Homo sapiens) Explore Q92692  Go to UniProtKB:  Q92692
PHAROS:  Q92692 GTEx:  ENSG00000130202

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.907	α = 90
b = 49.261	β = 116.98
c = 51.867	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Ramagopal, U.A., Samanta, D., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-02-06
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary