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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poliovirus receptor-related protein 4
A, B
133Homo sapiensGene Names: PVRL4 (LNIR, PRR4)
Find proteins for Q96NY8 (Homo sapiens)
Go to UniProtKB:  Q96NY8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.222 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 35.193α = 90.00
b = 35.193β = 90.00
c = 205.331γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CBASSdata collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Structure summary
  • Version 1.2: 2017-11-15
    Type: Refinement description