4JJH

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 4
A, B
133Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.193α = 90
b = 35.193β = 90
c = 205.331γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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