2AOG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

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: 10.1111/j.1742-4658.2005.04923.x
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE (RETROPEPSIN)
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 6 
Gene Names: gag-pol
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04587
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
ACY
Query on ACY

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A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
2NC
Query on 2NC

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A
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
p2/NC
C35 H68 N11 O8
MQPXOVRKKPPKFZ-QYKDHROSSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2NCKi: 530 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.020α = 90.00
b = 85.893β = 90.00
c = 46.614γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
MAR345data collection
SHELXphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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