4YOA

Crsystal structure HIV-1 Protease MDR769 L33F Complexed with darunavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops.

Kuiper, B.D.Keusch, B.J.Dewdney, T.G.Chordia, P.Ross, K.Brunzelle, J.S.Kovari, I.A.MacArthur, R.Salimnia, H.Kovari, L.C.

(2015) Biochem Biophys Rep 2: 160-165

  • DOI: 10.1016/j.bbrep.2015.06.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 protease (PR) is a 99 amino acid protein responsible for proteolytic processing of the viral polyprotein - an essential step in the HIV-1 life cycle. Drug resistance mutations in PR that are selected during antiretroviral therapy lead to reduce ...

    HIV-1 protease (PR) is a 99 amino acid protein responsible for proteolytic processing of the viral polyprotein - an essential step in the HIV-1 life cycle. Drug resistance mutations in PR that are selected during antiretroviral therapy lead to reduced efficacy of protease inhibitors (PI) including darunavir (DRV). To identify the structural mechanisms associated with the DRV resistance mutation L33F, we performed X-ray crystallographic studies with a multi-drug resistant HIV-1 protease isolate that contains the L33F mutation (MDR769 L33F). In contrast to other PR L33F DRV complexes, the structure of MDR769 L33F complexed with DRV reported here displays the protease flaps in an open conformation. The L33F mutation increases noncovalent interactions in the hydrophobic pocket of the PR compared to the wild-type (WT) structure. As a result, L33F appears to act as a molecular anchor, reducing the flexibility of the 30s loop (residues 29-35) and the 80s loop (residues 79-84). Molecular anchoring of the 30s and 80s loops leaves an open S1/S1' subsite and distorts the conserved hydrogen-bonding network of DRV. These findings are consistent with previous reports despite structural differences with regards to flap conformation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Protease
A
99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: pol
Find proteins for Q5RTL1 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5RTL1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download SDF File 
Download CCD File 
A
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
Darunavir, TMC114, UIC-94017
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.697 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 45.470α = 90.00
b = 45.470β = 90.00
c = 102.220γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary