Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 114.33 kDa 
• Atom Count: 7426 
• Modelled Residue Count: 953 
• Deposited Residue Count: 984 
• Unique protein chains: 2

3HVT

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

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

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Mutation(s): No 


• 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: 2.90 Å
• R-Value Work: 0.266 
• R-Value Observed: 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 U S A 91: 3911-3915

• PubMed: 7513427 
• 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 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: 

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)	A	556	Human immunodeficiency virus 1	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)	B	428	Human immunodeficiency virus 1	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NVP	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

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 = 223.6	α = 90
b = 69.9	β = 106.4
c = 105.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance