Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114326.19 
• Atom Count: 7426 
• Residue Count: 984 
• Unique protein chains: 2

3HVT

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

• DOI: 10.2210/pdb3HVT/pdb
• Entry 3HVT supersedes 2HVT

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B


• Deposited: 1994-07-25 Released: 1994-10-15 
• Deposition Author(s): Steitz, T.A., Smerdon, S.J., Jaeger, J., Wang, J., Kohlstaedt, L.A., Chirino, A.J., Friedman, J.M., Rice, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.266 

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.Usa 91: 3911-3915

• PubMed: 7513427 


• 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 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.

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Related Citations: 

• 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.USA 91: 3911
• 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
• 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 --: --
• 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 Harbor Symp.Quant.Biol. 58: 495




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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
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)	A	556	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)	B	428	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NVP	A	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE C15 H14 N4 O NQDJXKOVJZTUJA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Work: 0.266 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 223.600	α = 90.00
b = 69.900	β = 106.40
c = 105.500	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-25 
• Released Date: 1994-10-15 
• Deposition Author(s): Steitz, T.A., Smerdon, S.J., Jaeger, J., Wang, J., Kohlstaedt, L.A., Chirino, A.J., Friedman, J.M., Rice, P.A.
• This entry supersedes: 2HVT

Revision History 

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