Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants.

Yedidi, R.S.Proteasa, G.Martinez, J.L.Vickrey, J.F.Martin, P.D.Wawrzak, Z.Liu, Z.Kovari, I.A.Kovari, L.C.

(2011) Acta Crystallogr D Biol Crystallogr 67: 524-532

  • DOI: https://doi.org/10.1107/S0907444911011541
  • Primary Citation of Related Structures:  
    3OQ7, 3OQA, 3OQD, 3PJ6

  • PubMed Abstract: 

    The flexible flaps and the 80s loops (Pro79-Ile84) of HIV-1 protease are crucial in inhibitor binding. Previously, it was reported that the crystal structure of multidrug-resistant 769 (MDR769) HIV-1 protease shows a wide-open conformation of the flaps owing to conformational rigidity acquired by the accumulation of mutations. In the current study, the effect of mutations on the conformation of the 80s loop of MDR769 HIV-1 protease variants is reported. Alternate conformations of Pro81 (proline switch) with a root-mean-square deviation of 3-4.8 Å in the C(α) atoms of the I10V mutant and a side chain with a `flipped-out' conformation in the A82F mutant cause distortion in the S1/S1' binding pockets that affects inhibitor binding. The A82S and A82T mutants show local changes in the electrostatics of inhibitor binding owing to the mutation from nonpolar to polar residues. In summary, the crystallographic studies of four variants of MDR769 HIV-1 protease presented in this article provide new insights towards understanding the drug-resistance mechanism as well as a basis for design of future protease inhibitors with enhanced potency.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Protease99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for P35963 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35963 
Go to UniProtKB:  P35963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35963
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.534α = 90
b = 45.534β = 90
c = 101.926γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description