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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
A
556Human 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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
B
428Human 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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEVIC50:  300   nM  BindingDB
NEVEC50:  110   nM  BindingDB
NEVKi:  10000   nM  BindingDB
NEVKi:  9000   nM  BindingDB
NEVIC50:  6650   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  11300   nM  BindingDB
NEVIC50:  11800   nM  BindingDB
NEVEC50:  100   nM  BindingDB
NEVIC50:  60   nM  BindingDB
NEVKi:  18000   nM  BindingDB
NEVIC50:  13000   nM  BindingDB
NEVEC50:  250   nM  BindingDB
NEVIC50:  2.5999999046325684   nM  BindingDB
NEVIC50:  101   nM  BindingDB
NEVIC50:  20000   nM  BindingDB
NEVIC50:  23000   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  2110   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  1850   nM  BindingDB
NEVKi:  36000   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  3000   nM  BindingDB
NEVIC50:  3100   nM  BindingDB
NEVIC50:  3200   nM  BindingDB
NEVIC50:  2800   nM  BindingDB
NEVIC50:  14000   nM  BindingDB
NEVEC50:  380   nM  BindingDB
NEVIC50:  3800   nM  BindingDB
NEVIC50:  3930   nM  BindingDB
NEVIC50:  3500   nM  BindingDB
NEVEC50:  7500   nM  BindingDB
NEVIC50:  6000   nM  BindingDB
NEVIC50:  6440   nM  BindingDB
NEVIC50:  5500   nM  BindingDB
NEVIC50:  5750   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  4848   nM  BindingDB
NEVIC50:  500   nM  BindingDB
NEVIC50:  430   nM  BindingDB
NEVIC50:  700   nM  BindingDB
NEVIC50:  640   nM  BindingDB
NEVIC50:  600   nM  BindingDB
NEVIC50:  1100   nM  BindingDB
NEVEC50:  3900   nM  BindingDB
NEVIC50:  690   nM  BindingDB
NEVIC50:  2600   nM  BindingDB
NEVIC50:  860   nM  BindingDB
NEVKi:  2000   nM  BindingDB
NEVIC50:  1700   nM  BindingDB
NEVIC50:  1480   nM  BindingDB
NEVIC50:  1300   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  100   nM  BindingDB
NEVEC50:  30   nM  BindingDB
NEVIC50:  200   nM  BindingDB
NEVIC50:  180   nM  BindingDB
NEVEC50:  20   nM  BindingDB
NEVIC50:  170   nM  BindingDB
NEVEC50:  26   nM  BindingDB
NEVIC50:  270   nM  BindingDB
NEVIC50:  250   nM  BindingDB
NEVEC50:  70   nM  BindingDB
NEVIC50:  230   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVIC50:  320   nM  BindingDB
NEVEC50:  52   nM  BindingDB
NEVEC50:  53   nM  BindingDB
NEVIC50:  300   nM  BindingDB
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 

  • 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