4JJH | pdb_00004jjh

Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]

• PDB DOI: https://doi.org/10.2210/pdb4JJH/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-03-07 Released: 2013-03-27 
• Deposition Author(s): Kumar, P.R., Bonanno, J., Ahmed, M., Banu, R., Bhosle, R., Calarese, D., Celikigil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S., Glenn, A.S., Hillerich, B., Khafizov, K., Love, J., Patel, H., Seidel, R., Stead, M., Toro, R., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the D1 domain of human Nectin-4 extracellular fragment [NYSGRC-005624]

Kumar, P.R., Nathenson, S.G., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.94 kDa 
• Atom Count: 1,727 
• Modeled Residue Count: 223 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poliovirus receptor-related protein 4	A, B	133	Homo sapiens	Mutation(s): 0  Gene Names: LNIR, Nectin-4, PRR4, PVRL4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY8 (Homo sapiens) Explore Q96NY8  Go to UniProtKB:  Q96NY8
PHAROS:  Q96NY8 GTEx:  ENSG00000143217

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.193	α = 90
b = 35.193	β = 90
c = 205.331	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Kumar, P.R., Bonanno, J., Ahmed, M., Banu, R., Bhosle, R., Calarese, D., Celikigil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S., Glenn, A.S., Hillerich, B., Khafizov, K., Love, J., Patel, H., Seidel, R., Stead, M., Toro, R., 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: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary