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Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine
Biology and Chemistry Report
4PWD
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE, HYDROLASE/DNA/RNA/INHIBITOR
    Text fingers, palm, thumb, connection, RNase H, nucleotidyltransferase, DNA-directed DNA polymerase, RNA-directed DNA polymerase, nuclease, Ribonuclease H, tRNA, TRANSFERASE, HYDROLASE-DNA-RNA-INHIBITOR complex

    Polymeric Molecules

    Chain A,C
    Description HIV-1 Reverse Transcriptase, P66 subunit 
    Fragment UNP residues 600-1153 
    Mutation Q258C, C280S, D498N 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 64023.1 
    Source Method genetically manipulated  
    Entity Name Reverse transcriptase/ribonuclease H, Exoribonuclease H, p66 RT 
    Chain B,D
    Description HIV-1 Reverse Transcriptase, P51 subunit 
    Fragment UNP residues 600-1027 
    Mutation C280S 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 50040.1 
    Source Method genetically manipulated  
    Entity Name p51 RT 
    Chain E,T
    Description 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 8743.3 
    Source Method synthetic  
    Chain F,P
    Description 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 6416.2 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    NVP  11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE  C15 H14 N4 O   266.30  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C POL_HV1B1 P03366     
    B,D POL_HV1B1 P03366     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A C  2.7.7.49      
    A C  2.7.7.7      
    A C  3.1.13.2      
    A C  3.1.26.13      
    B D  2.7.7.49      
    B D  2.7.7.7      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    6278   RNA Dependent DNA Replication  A DNA Replication Process That Uses RNA As a Template For RNA Dependent DNA Polymerases (e.g. Reverse Transcriptase) That Synthesize the New Strands. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    3964   RNA Directed DNA Polymerase Activity  Catalysis of the Reaction: Deoxynucleoside Triphosphate + Dna(n) = Diphosphate + Dna(n+1). Catalyzes RNA Template Directed Extension of the 3' End of a DNA Strand by One Deoxynucleotide At a Time. 
    4523   RNA DNA Hybrid Ribonuclease Activity  Catalysis of the Endonucleolytic Cleavage of RNA in RNA DNA Hybrids to 5' Phosphomonoesters. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    6278   RNA Dependent DNA Replication  A DNA Replication Process That Uses RNA As a Template For RNA Dependent DNA Polymerases (e.g. Reverse Transcriptase) That Synthesize the New Strands. 
    3964   RNA Directed DNA Polymerase Activity  Catalysis of the Reaction: Deoxynucleoside Triphosphate + Dna(n) = Diphosphate + Dna(n+1). Catalyzes RNA Template Directed Extension of the 3' End of a DNA Strand by One Deoxynucleotide At a Time. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name Hiv 1
    Scientific Name Human immunodeficiency virus type 1  
    Strain BH10
    Gene gag-pol
    Host Scientific Name Escherichia coli  
    Host Vector Type Plasmid


    Chain A,C
    Common Name Hiv 1
    Scientific Name Human immunodeficiency virus type 1  
    Strain BH10
    Gene gag-pol
    Host Scientific Name Escherichia coli  
    Host Vector Type Plasmid