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HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B
Biology and Chemistry Report
1G9N
  •   Structure Details   Hide

    Structure Keywords

    Keywords Viral protein/Immune system
    Text COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB), HIV-1 EXTERIOR ENVELOPE GP120 FROM CLINICAL PRIMARY ISOLATE, YU2, T-CELL SURFACE GLYCOPROTEIN CD4, ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B, Viral protein-Immune system COMPLEX

    Polymeric Molecules

    Chain G
    Description ENVELOPE GLYCOPROTEIN GP120 
    Fragment CORE 
    Mutation VARIABLE LOOPS SUBSTITUTED 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34839.0 
    Source Method genetically manipulated  
    Chain C
    Description T-CELL SURFACE GLYCOPROTEIN CD4 
    Fragment D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 
    Mutation S184N, I185T 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 20503.4 
    Source Method genetically manipulated  
    Chain L
    Description ANTIBODY 17B, LIGHT CHAIN 
    Fragment ANTIGEN-BINDING FRAGMENT, FAB 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23440.2 
    Source Method genetically manipulated  
    Chain H
    Description ANTIBODY 17B, HEAVY CHAIN 
    Fragment ANTIGEN-BINDING FRAGMENT, FAB 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24525.7 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    NDG  2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    C CD4_HUMAN B2R737     
    G ENV_HV1Y2 P35961     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 164069    
     
  •   Gene Details   Hide

    Genetic Source

    Chain H
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Common Name House Mouse
    Host Scientific Name Mus musculus  
    Host Genus Mus
    Description Epstein Barr Virus Immortalized B Cell Clone Fused with a Murine B Cell Fusion Partner


    Chain L
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Common Name House Mouse
    Host Scientific Name Mus musculus  
    Host Genus Mus
    Description Epstein Barr Virus Immortalized B Cell Clone Fused with a Murine B Cell Fusion Partner


    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Common Name Chinese Hamster
    Host Scientific Name Cricetulus griseus  
    Host Genus Cricetulus
    Host Cell Type Ovary Cells (cho)


    Chain G
    Scientific Name Human immunodeficiency virus 1  
    Genus Lentivirus
    Strain CLADE B
    Variant Primary Isolate Yu2
    Host Common Name Fruit Fly
    Host Scientific Name Drosophila melanogaster  
    Host Genus Drosophila
    Description Secreted From Drosophila Schneider 2 Lines Under Control of an Inducible Metallothionein Promoter;


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12p13.31 920     CD4 molecule CD4    

    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
    rs199890832 LS-SNP   dbSNP   C 34 I - > K Coil 29% (Intermediate) 12 6909599
    rs201991979 LS-SNP   dbSNP   C 40 Q - > R Bend 4% (Buried) 12 6909617
    rs200264344 LS-SNP   dbSNP   C 54 R - > C 3/10 Helix 7% (Buried) 12 6923328
    rs201343243 LS-SNP   dbSNP   C 55 A - > ST Beta Ladder 0% (Buried) 12 6923331
    rs200573785 LS-SNP   dbSNP   C 56 D - > V Beta Ladder 34% (Intermediate) 12 6923335
    rs141281945 LS-SNP   dbSNP   C 70 I - > T Beta Ladder 7% (Buried) 12 6923377
    rs201280254 LS-SNP   dbSNP   C 79 S - > T Coil 12% (Intermediate) 12 6923403
    rs202208698 LS-SNP   dbSNP   C 111 G - > R Beta 30% (Intermediate) 12 6923957
    rs202028153 LS-SNP   dbSNP   C 122 P - > S Turn 99% (Exposed) 12 6923990
    rs201323005 LS-SNP   dbSNP   C 123 G - > D Turn 111% (Exposed) 12 6923994
    rs200491526 LS-SNP   dbSNP   C 138 I - > M Coil 23% (Intermediate) 12 6924040
    rs191620221 LS-SNP   dbSNP   C 139 Q - > E Beta Ladder 78% (Exposed) 12 6924041
    rs201435903 LS-SNP   dbSNP   C 140 G - > V Beta Ladder 12% (Intermediate) 12 6924045
    rs201423104 LS-SNP   dbSNP   C 142 K - > T Bend 40% (Exposed) 12 6924051
    rs200162977 LS-SNP   dbSNP   C 146 V - > M Beta Ladder 1% (Buried) 12 6924062
    rs201315085 LS-SNP   dbSNP   C 161 V - > L Beta Ladder 0% (Buried) 12 6924107
    rs143646863 LS-SNP   dbSNP   C 165 Q - > R Turn 88% (Exposed) 12 6924120
    rs28917504 LS-SNP   dbSNP   C 166 K - > E Beta 39% (Exposed) 12 6924122
    rs199799041 LS-SNP   dbSNP   C 172 I - > T Beta Ladder 18% (Intermediate) 12 6924141
    rs140406047 LS-SNP   dbSNP   C 175 V - > LM Beta Ladder 39% (Exposed) 12 6924149