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Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]
Biology and Chemistry Report
4JJH
  •   Structure Details   Hide

    Structure Keywords

    Keywords CELL ADHESION
    Text Nectin-4, Ig-like D1 domain, Ig superfamily, IMMUNE SYSTEM, Cell adhesion, Structural genomics, PSI-Biology, New York Structural Genomics Research Consortium, NYSGRC, Atoms-to-Animals: The Immune Function Network, IFN

    Polymeric Molecules

    Chain A,B
    Description Poliovirus receptor-related protein 4 
    Fragment D1 domain (UNP residues 32-153) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14439.2 
    Source Method genetically manipulated  
    Entity Name Ig superfamily receptor LNIR, Nectin-4, Processed poliovirus receptor-related protein 4 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PVRL4_HUMAN Q96NY8     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene lnir, nectin-4, prr4, pvrl4
    Host Scientific Name Trichoplusia ni  
    Host Strain Hi5
    Host Vector Type Plasmid
    Host Plasmid Name pIEX


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q22-q23.2 81607     poliovirus receptor-related 4 PVRL4    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs150247524 LS-SNP   dbSNP   A 38 D - > E Bend 74% (Exposed) 1 161049705
    rs3737786 LS-SNP   dbSNP   A 53 F - > L Beta 52% (Exposed) 1 161049662
    rs200474573 LS-SNP   dbSNP   A 55 R - > Q Coil 89% (Exposed) 1 161049655
    rs142201196 LS-SNP   dbSNP   A 59 G - > D Coil 0% (Buried) 1 161049643
    rs139707654 LS-SNP   dbSNP   A 68 A - > D Beta Ladder 19% (Intermediate) 1 161049616
    rs143991457 LS-SNP   dbSNP   A 68 A - > S Beta Ladder 19% (Intermediate) 1 161049617
    rs142765500 LS-SNP   dbSNP   A 85 K - > R Turn 78% (Exposed) 1 161049565
    rs35434391 LS-SNP   dbSNP   A 104 P - > T Bend 101% (Exposed) 1 161049509
    rs78105657 LS-SNP   dbSNP   A 107 P - > L Turn 54% (Exposed) 1 161049499
    rs77444104 LS-SNP   dbSNP   A 146 L - > M Beta Ladder 10% (Intermediate) 1 161049383