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Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility
Biology and Chemistry Report
3JWD
  •   Structure Details   Hide

    Structure Keywords

    Keywords VIRAL PROTEIN
    Text HIV-1 VIRAL SPIKE, MOLECULAR MOTION, PROTEIN ARCHITECTURE, RECEPTOR-TRIGGERED ENTRY, TYPE 1 FUSION PROTEIN, CELL MEMBRANE, DISULFIDE BOND, GLYCOPROTEIN, HOST-VIRUS INTERACTION, IMMUNE RESPONSE, VIRAL PROTEIN

    Polymeric Molecules

    Chain A,B
    Description HIV-1 GP120 ENVELOPE GLYCOPROTEIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 42118.0 
    Source Method genetically manipulated  
    Chain C,D
    Description T-cell surface glycoprotein CD4 
    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 L,O
    Description FAB 48D LIGHT CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 23252.9 
    Source Method genetically manipulated  
    Chain H,P
    Description FAB 48D HEAVY CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23515.5 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    C,D CD4_HUMAN B2R737     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 164076    
     
  •   Gene Details   Hide

    Genetic Source

    Chain H,P
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Unidentified herpesvirus  
    Host Cell Type Immortalized B Cell Clone Fused with a Murine B Cell Fusion Partner


    Chain L,O
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Unidentified herpesvirus  
    Host Cell Type Immortalized B Cell Clone Fused with a Murine B Cell Fusion Partner


    Chain C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cd4
    Host Common Name Chinese Hamster
    Host Scientific Name Cricetulus griseus  


    Chain A,B
    Scientific Name Human immunodeficiency virus 1  
    Strain HXBC2
    Host Common Name Fruit Fly
    Host Scientific Name Drosophila melanogaster  
    Host Vector Type Plasmid
    Host Plasmid Name PMT


    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
    rs202129605 LS-SNP   dbSNP   C 1000 G - > E Coil 121% (Exposed) 12 6909497
    rs199890832 LS-SNP   dbSNP   C 1034 I - > K Coil 23% (Intermediate) 12 6909599
    rs201991979 LS-SNP   dbSNP   C 1040 Q - > R Bend 6% (Buried) 12 6909617
    rs200264344 LS-SNP   dbSNP   C 1054 R - > C Turn 8% (Buried) 12 6923328
    rs201343243 LS-SNP   dbSNP   C 1055 A - > ST Beta 1% (Buried) 12 6923331
    rs200573785 LS-SNP   dbSNP   C 1056 D - > V Coil 28% (Intermediate) 12 6923335
    rs141281945 LS-SNP   dbSNP   C 1070 I - > T Beta Ladder 24% (Intermediate) 12 6923377
    rs201280254 LS-SNP   dbSNP   C 1079 S - > T Coil 20% (Intermediate) 12 6923403
    rs202208698 LS-SNP   dbSNP   C 1111 G - > R Beta Ladder 12% (Intermediate) 12 6923957
    rs202028153 LS-SNP   dbSNP   C 1122 P - > S Bend 88% (Exposed) 12 6923990
    rs201323005 LS-SNP   dbSNP   C 1123 G - > D Bend 98% (Exposed) 12 6923994
    rs200491526 LS-SNP   dbSNP   C 1138 I - > M Beta Ladder 22% (Intermediate) 12 6924040
    rs191620221 LS-SNP   dbSNP   C 1139 Q - > E Beta Ladder 67% (Exposed) 12 6924041
    rs201435903 LS-SNP   dbSNP   C 1140 G - > V Beta Ladder 21% (Intermediate) 12 6924045
    rs201423104 LS-SNP   dbSNP   C 1142 K - > T Bend 58% (Exposed) 12 6924051
    rs200162977 LS-SNP   dbSNP   C 1146 V - > M Beta Ladder 18% (Intermediate) 12 6924062
    rs201315085 LS-SNP   dbSNP   C 1161 V - > L Beta Ladder 0% (Buried) 12 6924107
    rs143646863 LS-SNP   dbSNP   C 1165 Q - > R Turn 89% (Exposed) 12 6924120
    rs28917504 LS-SNP   dbSNP   C 1166 K - > E Beta Ladder 68% (Exposed) 12 6924122
    rs199799041 LS-SNP   dbSNP   C 1172 I - > T Beta Ladder 15% (Intermediate) 12 6924141
    rs140406047 LS-SNP   dbSNP   C 1175 V - > LM Coil 63% (Exposed) 12 6924149