Crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog P2-NC

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 

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Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs.

Tie, Y.Boross, P.I.Wang, Y.F.Gaddis, L.Liu, F.Chen, X.Tozser, J.Harrison, R.W.Weber, I.T.

(2005) FEBS J 272: 5265-5277

  • DOI: https://doi.org/10.1111/j.1742-4658.2005.04923.x
  • Primary Citation of Related Structures:  
    2AOC, 2AOD, 2AOE, 2AOF, 2AOG, 2AOH, 2AOI, 2AOJ

  • PubMed Abstract: 

    HIV-1 protease (PR) and two drug-resistant variants--PR with the V82A mutation (PR(V82A)) and PR with the I84V mutation (PR(I84V))--were studied using reduced peptide analogs of five natural cleavage sites (CA-p2, p2-NC, p6pol-PR, p1-p6 and NC-p1) to understand the structural and kinetic changes. The common drug-resistant mutations V82A and I84V alter residues forming the substrate-binding site. Eight crystal structures were refined at resolutions of 1.10-1.60 A. Differences in the PR-analog interactions depended on the peptide sequence and were consistent with the relative inhibition. Analog p6(pol)-PR formed more hydrogen bonds of P2 Asn with PR and fewer van der Waals contacts at P1' Pro compared with those formed by CA-p2 or p2-NC in PR complexes. The P3 Gly in p1-p6 provided fewer van der Waals contacts and hydrogen bonds at P2-P3 and more water-mediated interactions. PR(I84V) showed reduced van der Waals interactions with inhibitor compared with PR, which was consistent with kinetic data. The structures suggest that the binding affinity for mutants is modulated by the conformational flexibility of the substrate analogs. The complexes of PR(V82A) showed smaller shifts of the main chain atoms of Ala82 relative to PR, but more movement of the peptide analog, compared to complexes with clinical inhibitors. PR(V82A) was able to compensate for the loss of interaction with inhibitor caused by mutation, in agreement with kinetic data, but substrate analogs have more flexibility than the drugs to accommodate the structural changes caused by mutation. Hence, these structures help to explain how HIV can develop drug resistance while retaining the ability of PR to hydrolyze natural substrates.

  • Organizational Affiliation

    Department of Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30302-4010, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus type 1 (BH5 ISOLATE)Mutation(s): 6 
Gene Names: POL
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04587
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2NC

Download Ideal Coordinates CCD File 
C [auth A]N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
C35 H68 N11 O8
Query on GOL

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E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B]
C3 H8 O3
Query on ACY

Download Ideal Coordinates CCD File 
C2 H4 O2
Query on UNX

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 85.893β = 90
c = 46.614γ = 90
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
SHELXmodel building
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-02-08
    Changes: Non-polymer description
  • Version 1.4: 2012-05-09
    Changes: Non-polymer description
  • Version 1.5: 2013-02-27
    Changes: Other
  • Version 1.6: 2017-10-11
    Changes: Refinement description
  • Version 1.7: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.8: 2023-08-23
    Changes: Data collection, Refinement description