3HVT

STRUCTURAL BASIS OF ASYMMETRY IN THE HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE HETERODIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1.

Smerdon, S.J.Jager, J.Wang, J.Kohlstaedt, L.A.Chirino, A.J.Friedman, J.M.Rice, P.A.Steitz, T.A.

(1994) Proc Natl Acad Sci U S A 91: 3911-3915

  • DOI: 10.1073/pnas.91.9.3911
  • Primary Citation of Related Structures:  
    3HVT

  • PubMed Abstract: 
  • The dipyridodiazepinone Nevirapine is a potent and highly specific inhibitor of the reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1). It is a member of an important class of nonnucleoside drugs that appear to share part or all of the same binding site on the enzyme but are susceptible to a variety of spontaneous drug-resistance mutations ...

    The dipyridodiazepinone Nevirapine is a potent and highly specific inhibitor of the reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1). It is a member of an important class of nonnucleoside drugs that appear to share part or all of the same binding site on the enzyme but are susceptible to a variety of spontaneous drug-resistance mutations. The co-crystal-structure of HIV-1 RT and Nevirapine has been solved previously at 3.5-A resolution and now is partially refined against data extending to 2.9-A spacing. The drug is bound in a hydrophobic pocket and in contact with some 38 protein atoms from the p66 palm and thumb subdomains. Most, but not all, nonnucleoside drug-resistance mutations map to residues in close contact with Nevirapine. The major effects of these mutations are to introduce steric clashes with the drug molecule or to remove favorable protein-drug contacts. Additionally, four residues (Phe-227, Trp-229, Leu-234, and Tyr-319) in contact with Nevirapine have not been selected as sites of drug-resistance mutations, implying that there may be limitations on the number and types of resistance mutations that yield viable virus. Strategies of inhibitor design that target interactions with these conserved residues may yield drugs that are less vulnerable to escape mutations.


    Related Citations: 
    • Comparison of Three Different Crystal Forms Shows HIV-1 Reverse Transcriptase Displays an Internal Swivel Motion
      Jaeger, J., Smerdon, S.J., Wang, J., Boisvert, D.C., Steitz, T.A.
      () To be published --: --
    • Structure of the Binding Site for Nonnucleoside Inhibitors of the Reverse Transcriptase of Human Immunodeficiency Virus Type 1
      Smerdon, S.J., Jaeger, J., Wang, J., Kohlstaedt, L.A., Chirino, A.J., Friedman, J., Rice, P.A., Steitz, T.A.
      (1994) Proc Natl Acad Sci U S A 91: 3911
    • Two DNA Polymerases: HIV Reverse Transcriptase and Klenow Fragment of E. Coli DNA Polymerase I. (In: DNA & Chromosomes: Abstracts of Papers Presented at the LVIII Cold Spring Harbor Symposium on Quantitative Biology)
      Steitz, T.A., Smerdon, S.J., Jaeger, J., Wang, J., Kohlstaedt, L.A., Friedman, J., Beese, L., Rice, P.A.
      (1993) Cold Spring Harb Symp Quant Biol 58: 495
    • Crystal Structure at 3.5 Angstroms Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor
      Kohlstaedt, L.A., Wang, J., Friedman, J.M., Rice, P.A., Steitz, T.A.
      (1992) Science 256: 1783

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)A556Human immunodeficiency virus 1Mutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)B428Human immunodeficiency virus 1Mutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download Ideal Coordinates CCD File 
C [auth A]11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.6α = 90
b = 69.9β = 106.4
c = 105.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-04
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance