Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface
DOI:10.2210/pdb4b3o/pdb   NDB ID: NA2190
4B3O
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/dna/rna
    Structure Weight: 132112.08
    Molecule: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
    Polymer: 1 Type: protein Length: 560
    Chains: A
    EC#: 2.7.7.49    2.7.7.7    3.1.26.13   
    Mutation: YES
    Organism: Human immunodeficiency virus 1
    Gene Name: gag-pol
    UniProtKB: Protein Feature View | Search PDB | P04585  
    Molecule: P51 RT
    Polymer: 2 Type: protein Length: 441
    Chains: B
    EC#: 2.7.7.49    2.7.7.7    3.1.26.13   
    Mutation: YES
    Organism: Human immunodeficiency virus 1
    Gene Name: gag-pol
    UniProtKB: Protein Feature View | Search PDB | P04585  
    Molecule: 5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3'
    Polymer: 3 Type: dna Length: 24
    Chains: D
    Organism: synthetic construct
    Molecule: 5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3'
    Polymer: 4 Type: rna Length: 27
    Chains: R
    Organism: synthetic construct
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Human immunodeficiency virus 1   Taxonomy   Common Name: Hiv-1 Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Human immunodeficiency virus 1   Taxonomy   Common Name: Hiv-1 Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 4
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1A30   HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR 
    1BV7   COUNTERACTING HIV-1 PROTEASE DRUG RESISTANCE: STRUCTURAL ANALYSIS OF MUTANT PROTEASES COMPLEXED WITH XV638 AND SD146, CYCLIC UREA AMIDES WITH BROAD SPECIFICITIES 
    1BV9   HIV-1 PROTEASE (I84V) COMPLEXED WITH XV638 OF DUPONT PHARMACEUTICALS 
    1BVE   HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR, 28 STRUCTURES 
    1BVG   HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR MINIMIZED AVERAGE STRUCTURE 
    1BWA   HIV-1 PROTEASE (V82F/I84V) DOUBLE MUTANT COMPLEXED WITH XV638 OF DUPONT PHARMACEUTICALS 
    1BWB   HIV-1 PROTEASE (V82F/I84V) DOUBLE MUTANT COMPLEXED WITH SD146 OF DUPONT PHARMACEUTICALS 
    1C0T   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH BM+21.1326 
    1C0U   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH BM+50.0934 
    1C1B   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GCA- 186 
    1C1C   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH TNK- 6123 
    1DMP   STRUCTURE OF HIV-1 PROTEASE COMPLEX 
    1DTQ   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-1 (PETT131A94) 
    1DTT   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-2 (PETT130A94) 
    1E6J   CRYSTAL STRUCTURE OF HIV-1 CAPSID PROTEIN (P24) IN COMPLEX WITH FAB13B5 
    1EP4   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH S-1153 
    1ESK   SOLUTION STRUCTURE OF NCP7 FROM HIV-1 
    1EX4   HIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN 
    1EXQ   CRYSTAL STRUCTURE OF THE HIV-1 INTEGRASE CATALYTIC COREDOMAIN 
    1FB7   CRYSTAL STRUCTURE OF AN IN VIVO HIV-1 PROTEASE MUTANT INCOMPLEX WITH SAQUINAVIR: INSIGHTS INTO THE MECHANISMS OFDRUG RESISTANCE 
    1FK9   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH DMP-266(EFAVIRENZ) 
    1FKO   CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ) 
    1FKP   CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV- 1REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1G6L   1.9A CRYSTAL STRUCTURE OF TETHERED HIV-1 PROTEASE 
    1HIV   HIV-1 PROTEASE (HIV-1 PR) COMPLEX WITH U75875 (NOA- HIS-CHA-PSI[CH(OH)CH(OH)]VAL-ILE-APY) 
    1HVH   NONPEPTIDE CYCLIC CYANOGUANIDINES AS HIV PROTEASE INHIBITORS 
    1HVR   HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) PROTEASE COMPLEXED WITH XK263 OF DUPONT MERCK 
    1HWR   MOLECULAR RECOGNITION OF CYCLIC UREA HIV PROTEASE INHIBITORS 
    1HXB   HIV-1 PROTEINASE COMPLEXED WITH RO 31-8959 
    1JKH   CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ) 
    1JLA   CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH TNK-651 
    1JLB   CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1JLC   CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH PETT-2 
    1JLE   CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE 
    1JLF   CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1JLG   CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781 
    1JLQ   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH 739W94 
    1KLM   HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH BHAP U- 90152 
    1LV1   CRYSTAL STRUCTURE ANALYSIS OF THE NON-ACTIVE SITE MUTANT OFTETHERED HIV-1 PROTEASE TO 2.1A RESOLUTION 
    1LW0   CRYSTAL STRUCTURE OF T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1LW2   CRYSTAL STRUCTURE OF T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH 1051U91 
    1LWC   CRYSTAL STRUCTURE OF M184V MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1LWE   CRYSTAL STRUCTURE OF M41L/T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE (RTMN) IN COMPLEX WITH NEVIRAPINE 
    1LWF   CRYSTAL STRUCTURE OF A MUTANT HIV-1 REVERSE TRANSCRIPTASE(RTMQ+M184V: M41L/D67N/K70R/M184V/T215Y) IN COMPLEX WITHNEVIRAPINE 
    1NCP    
    1O1W   SOLUTION STRUCTURE OF THE RNASE H DOMAIN OF THE HIV -1REVERSE TRANSCRIPTASE IN THE PRESENCE OF MAGNESIUM 
    1ODW   NATIVE HIV-1 PROTEINASE 
    1ODY   HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 
    1QBR   HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY 
    1QBS   HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY 
    1QBT   HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY 
    1QBU   HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY 
    1REV   HIV-1 REVERSE TRANSCRIPTASE 
    1RT1   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH MKC-442 
    1RT2   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH TNK-651 
    1RT3   AZT DRUG RESISTANT HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH 1051U91 
    1RT4   HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC781 
    1RT5   HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC10 
    1RT6   HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC38 
    1RT7   HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC84 
    1RTD   STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE 
    1RTH    
    1RTI    
    1RTJ    
    1S1T   CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781 
    1S1U   CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1S1V   CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH TNK-651 
    1S1W   CRYSTAL STRUCTURE OF V106A MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781 
    1S1X   CRYSTAL STRUCTURE OF V108I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE 
    1T05   HIV-1 REVERSE TRANSCRIPTASE CROSSLINKED TO TEMPLATE- PRIMERWITH TENOFOVIR-DIPHOSPHATE BOUND AS THE INCOMINGNUCLEOTIDE SUBSTRATE 
    1TAM   HUMAN IMMUNODEFICIENCY VIRUS, NMR, MINIMIZED AVERAGE STRUCTURE 
    1TKT   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW426318 
    1TKX   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW490745 
    1TKZ   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW429576 
    1TL1   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW451211 
    1TL3   CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW450557 
    1VRT    
    1VRU    
    2WHH   HIV-1 PROTEASE TETHERED DIMER Q-PRODUCT COMPLEX ALONG WITH NUCLEOPHILIC WATER MOLECULE 
    2WOM   CRYSTAL STRUCTURE OF UK-453061 BOUND TO HIV-1 REVERSE TRANSCRIPTASE (K103N). 
    2WON   CRYSTAL STRUCTURE OF UK-453061 BOUND TO HIV-1 REVERSE TRANSCRIPTASE (WILD-TYPE). 
    3PHV   HIV-1 PROTEASE (ISOLATE HXB2) 
    4B37   STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE 
    4B3P   STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE 
    4B3Q   STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    EFZ
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    EFZ C14 H9 Cl F3 N O2
    (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL- 1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
    EFZ:4B3O
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    EFZ
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    EFZ
    EC50: 1 - 300 nM (98) - data from BindingDB  
    IC50: 0.75 - 3400 nM (98) - data from BindingDB  
    Ki: 3 - 380 nM (98) - data from BindingDB  
    N/Ain BindingMoad
    N/Ain PDBbind
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    3DR
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    3DR C5 H11 O6 P dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA2190
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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