1RQ9

Crystal structures of a Multidrug-Resistant HIV-1 Protease Reveal an Expanded Active Site Cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity.

Logsdon, B.C.Vickrey, J.F.Martin, P.Proteasa, G.Koepke, J.I.Terlecky, S.R.Wawrzak, Z.Winters, M.A.Merigan, T.C.Kovari, L.C.

(2004) J Virol 78: 3123-3132

  • DOI: 10.1128/jvi.78.6.3123-3132.2004
  • Primary Citation of Related Structures:  
    1RV7, 1RPI, 1RQ9

  • PubMed Abstract: 
  • The goal of this study was to use X-ray crystallography to investigate the structural basis of resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors. We overexpressed, purified, and crystallized a multidrug-resistant (MDR) HIV ...

    The goal of this study was to use X-ray crystallography to investigate the structural basis of resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors. We overexpressed, purified, and crystallized a multidrug-resistant (MDR) HIV-1 protease enzyme derived from a patient failing on several protease inhibitor-containing regimens. This HIV-1 variant contained codon mutations at positions 10, 36, 46, 54, 63, 71, 82, 84, and 90 that confer drug resistance to protease inhibitors. The 1.8-angstrom (A) crystal structure of this MDR patient isolate reveals an expanded active-site cavity. The active-site expansion includes position 82 and 84 mutations due to the alterations in the amino acid side chains from longer to shorter (e.g., V82A and I84V). The MDR isolate 769 protease "flaps" stay open wider, and the difference in the flap tip distances in the MDR 769 variant is 12 A. The MDR 769 protease crystal complexes with lopinavir and DMP450 reveal completely different binding modes. The network of interactions between the ligands and the MDR 769 protease is completely different from that seen with the wild-type protease-ligand complexes. The water molecule-forming hydrogen bonds bridging between the two flaps and either the substrate or the peptide-based inhibitor are lacking in the MDR 769 clinical isolate. The S1, S1', S3, and S3' pockets show expansion and conformational change. Surface plasmon resonance measurements with the MDR 769 protease indicate higher k(off) rates, resulting in a change of binding affinity. Surface plasmon resonance measurements provide k(on) and k(off) data (K(d) = k(off)/k(on)) to measure binding of the multidrug-resistant protease to various ligands. This MDR 769 protease represents a new antiviral target, presenting the possibility of designing novel inhibitors with activity against the open and expanded protease forms.


    Related Citations: 
    • HIV-1 protease variants from 100-fold drug resistant clinical isolates: expression, purification, and crystallization.
      Vickrey, J.F., Logsdon, B.C., Proteasa, G., Palmer, S., Winters, M.A., Merigan, T.C., Kovari, L.C.
      (2003) Protein Expr Purif 28: 165

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
proteaseAB99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: HIV-1pol
EC: 3.4.23.16
Find proteins for Q5RTL1 (Human immunodeficiency virus 1)
Explore Q5RTL1 
Go to UniProtKB:  Q5RTL1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMQ
Query on DMQ

Download CCD File 
B
[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-1,3-BIS([(3-AMINO)PHENYL]METHYL)-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPINONE
C33 H36 N4 O3
KYRSNWPSSXSNEP-ZRTHHSRSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMQKi:  0.3400000035762787   nM  BindingDB
DMQKi:  0.3100000023841858   nM  BindingDB
DMQKi:  0.3400000035762787   nM  BindingDB
DMQKi:  0.30000001192092896   nM  BindingDB
DMQKi:  0.2800000011920929   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.097α = 90
b = 45.097β = 90
c = 102.957γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance