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HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b
Biology and Chemistry Report
2NXY
  •   Structure Details   Hide

    Structure Keywords

    Keywords VIRAL PROTEIN/IMMUNE SYSTEM
    Text HIV, gp120, antibody, CD4, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX

    Polymeric Molecules

    Chain A
    Description ENVELOPE GLYCOPROTEIN GP120 
    Fragment CORE 
    Mutation S334A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35041.0 
    Source Method genetically manipulated  
    Chain B
    Description T-cell surface glycoprotein CD4 
    Fragment D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 20419.4 
    Source Method genetically manipulated  
    Entity Name T-cell surface antigen T4/Leu-3 
    Chain C
    Description ANTIBODY 17B, LIGHT CHAIN 
    Fragment ANTIGEN-BINDING FRAGMENT, FAB 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23400.1 
    Source Method genetically manipulated  
    Chain D
    Description ANTIBODY 17B, HEAVY CHAIN 
    Fragment ANTIGEN-BINDING FRAGMENT, FAB 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24457.6 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    HEZ  HEXANE-1,6-DIOL  C6 H14 O2   118.17  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    TRS  2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL  C4 H12 N O3   122.14  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A Q49DS8_9HIV1 Q49DS8     
    B CD4_HUMAN B2R737     
    C Q6P5S8_HUMAN Q6P5S8     
    D Q6N095_HUMAN Q6N095     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 174342    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    19031   Viral Envelope  The Lipid Bilayer of a Virion That Surrounds the Protein Capsid. May Also Contain Glycoproteins. 
    Chain B
    GO ID   Ontology GO Term Definition
    7155   Cell Adhesion  The Attachment of a Cell Either to Another Cell or to an Underlying Substrate Such As the Extracellular Matrix Via Cell Adhesion Molecules. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Genus Homo
    Host Cell Line 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 Human
    Host Scientific Name Homo sapiens  
    Host Genus Homo
    Host Cell Line Epstein Barr Virus Immortalized B Cell Clone Fused with a Murine B Cell Fusion Partner


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene cd4
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain A
    Scientific Name Human immunodeficiency virus 1  
    Genus Lentivirus
    Strain HXBC2
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Genus Homo
    Host Cell Line Embryonic Cell Line 293
    Host Organ Kidney
    Host Vector Type Plasmid
    Host Plasmid Name CMVR


    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   B 1034 I - > K Coil 32% (Intermediate) 12 6909599
    rs201991979 LS-SNP   dbSNP   B 1040 Q - > R Beta Ladder 5% (Buried) 12 6909617
    rs200264344 LS-SNP   dbSNP   B 1054 R - > C 3/10 Helix 7% (Buried) 12 6923328
    rs201343243 LS-SNP   dbSNP   B 1055 A - > ST Beta Ladder 1% (Buried) 12 6923331
    rs200573785 LS-SNP   dbSNP   B 1056 D - > V Beta Ladder 48% (Exposed) 12 6923335
    rs141281945 LS-SNP   dbSNP   B 1070 I - > T Beta Ladder 16% (Intermediate) 12 6923377
    rs201280254 LS-SNP   dbSNP   B 1079 S - > T Coil 18% (Intermediate) 12 6923403
    rs202208698 LS-SNP   dbSNP   B 1111 G - > R Turn 38% (Exposed) 12 6923957
    rs202028153 LS-SNP   dbSNP   B 1122 P - > S Turn 96% (Exposed) 12 6923990
    rs201323005 LS-SNP   dbSNP   B 1123 G - > D Turn 108% (Exposed) 12 6923994
    rs200491526 LS-SNP   dbSNP   B 1138 I - > M Beta Ladder 18% (Intermediate) 12 6924040
    rs191620221 LS-SNP   dbSNP   B 1139 Q - > E Beta Ladder 67% (Exposed) 12 6924041
    rs201435903 LS-SNP   dbSNP   B 1140 G - > V Beta Ladder 37% (Exposed) 12 6924045
    rs201423104 LS-SNP   dbSNP   B 1142 K - > T Bend 54% (Exposed) 12 6924051
    rs200162977 LS-SNP   dbSNP   B 1146 V - > M Beta Ladder 6% (Buried) 12 6924062
    rs201315085 LS-SNP   dbSNP   B 1161 V - > L Beta Ladder 0% (Buried) 12 6924107
    rs143646863 LS-SNP   dbSNP   B 1165 Q - > R Turn 93% (Exposed) 12 6924120
    rs28917504 LS-SNP   dbSNP   B 1166 K - > E Beta Ladder 46% (Exposed) 12 6924122
    rs199799041 LS-SNP   dbSNP   B 1172 I - > T Beta Ladder 15% (Intermediate) 12 6924141
    rs140406047 LS-SNP   dbSNP   B 1175 V - > LM Coil 42% (Exposed) 12 6924149