1RQ9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.335 
  • R-Value Work: 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

  • Primary Citation of Related Structures:  1RPI, 1RV7

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protease
A, B
99Human immunodeficiency virus 1Gene 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
DMQ
Query on DMQ

Download SDF File 
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
DMP450(INHIBITOR OF DUPONT MERCK)
C33 H36 N4 O3
KYRSNWPSSXSNEP-ZRTHHSRSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMQKi: 0.3 - .34 nM (86) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.254 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 45.097α = 90.00
b = 45.097β = 90.00
c = 102.957γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4phasing
d*TREKdata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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