4NPU

Crystal Structure of HIV-1 Protease Multiple Mutant P51


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps.

Zhang, Y.Chang, Y.C.Louis, J.M.Wang, Y.F.Harrison, R.W.Weber, I.T.

(2014) Acs Chem.Biol. 9: 1351-1358

  • DOI: 10.1021/cb4008875
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The molecular basis for high resistance to clinical inhibitors of HIV-1 protease (PR) was examined for the variant designated PRP51 that was selected for resistance to darunavir (DRV). High resolution crystal structures of PRP51 with the active site ...

    The molecular basis for high resistance to clinical inhibitors of HIV-1 protease (PR) was examined for the variant designated PRP51 that was selected for resistance to darunavir (DRV). High resolution crystal structures of PRP51 with the active site D25N mutation revealed a ligand-free form and an inhibitor-bound form showing a unique binding site and orientation for DRV. This inactivating mutation is known to increase the dimer dissociation constant and decrease DRV affinity of PR. The PRP51-D25N dimers were in the open conformation with widely separated flaps, as reported for other highly resistant variants. PRP51-D25N dimer bound two DRV molecules and showed larger separation of 8.7 Å between the closest atoms of the two flaps compared with 4.4 Å for the ligand-free structure of this mutant. The ligand-free structure, however, lacked van der Waals contacts between Ile50 and Pro81' from the other subunit in the dimer, unlike the majority of PR structures. DRV is bound inside the active site cavity; however, the inhibitor is oriented almost perpendicular to its typical position and exhibits only 2 direct hydrogen bond and two water-mediated interactions with atoms of PRP51-D25N compared with 11 hydrogen bond interactions seen for DRV bound in the typical position in wild-type enzyme. The atypical location of DRV may provide opportunities for design of novel inhibitors targeting the open conformation of PR drug-resistant mutants.


    Organizational Affiliation

    Department of Chemistry, ‡Department of Biology, and §Department of Computer Science, Georgia State University , Atlanta, Georgia 30303, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 10 
Gene Names: pol
Find proteins for O38896 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38896
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 46.685α = 90.00
b = 46.685β = 90.00
c = 101.617γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-11-22 
  • Released Date: 2014-10-08 
  • Deposition Author(s): Zhang, Y., Weber, I.T.

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release