2P3D

Crystal Structure of the multi-drug resistant mutant subtype F HIV protease complexed with TL-3 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Characterization of B and non-B Subtypes of HIV-Protease: Insights into the Natural Susceptibility to Drug Resistance Development.

Sanches, M.Krauchenco, S.Martins, N.H.Gustchina, A.Wlodawer, A.Polikarpov, I.

(2007) J Mol Biol 369: 1029-1040

  • DOI: 10.1016/j.jmb.2007.03.049
  • Primary Citation of Related Structures:  
    2P3D, 2P3C, 2P3B, 2P3A

  • PubMed Abstract: 
  • Although a majority of HIV-1 infections in Brazil are caused by the subtype B virus (also prevalent in the United States and Western Europe), viral subtypes F and C are also found very frequently. Genomic differences between the subtypes give rise to ...

    Although a majority of HIV-1 infections in Brazil are caused by the subtype B virus (also prevalent in the United States and Western Europe), viral subtypes F and C are also found very frequently. Genomic differences between the subtypes give rise to sequence variations in the encoded proteins, including the HIV-1 protease. The current anti-HIV drugs have been developed primarily against subtype B and the effects arising from the combination of drug-resistance mutations with the naturally existing polymorphisms in non-B HIV-1 subtypes are only beginning to be elucidated. To gain more insights into the structure and function of different variants of HIV proteases, we have determined a 2.1 A structure of the native subtype F HIV-1 protease (PR) in complex with the protease inhibitor TL-3. We have also solved crystal structures of two multi-drug resistant mutant HIV PRs in complex with TL-3, from subtype B (Bmut) carrying the primary mutations V82A and L90M, and from subtype F (Fmut) carrying the primary mutation V82A plus the secondary mutation M36I, at 1.75 A and 2.8 A resolution, respectively. The proteases Bmut, Fwt and Fmut exhibit sevenfold, threefold, and 54-fold resistance to TL-3, respectively. In addition, the structure of subtype B wild type HIV-PR in complex with TL-3 has been redetermined in space group P6(1), consistent with the other three structures. Our results show that the primary mutation V82A causes the known effect of collapsing the S1/S1' pockets that ultimately lead to the reduced inhibitory effect of TL-3. Our results further indicate that two naturally occurring polymorphic substitutions in subtype F and other non-B HIV proteases, M36I and L89M, may lead to early development of drug resistance in patients infected with non-B HIV subtypes.


    Related Citations: 
    • Crystallization of a non-B and a B mutant HIV protease
      Sanches, M., Martins, N.H., Calazans, A., Brindeiro, R.M., Tanuri, A., Antunes, O.A.C., Polikarpov, I.
      (2004) Acta Crystallogr D Biol Crystallogr D60: 1625

    Organizational Affiliation

    Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense, 400, CEP 13560-970, São Carlos, SP, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pol proteinAB99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
EC: 3.4.23.16
Find proteins for Q7SRY5 (Human immunodeficiency virus 1)
Explore Q7SRY5 
Go to UniProtKB:  Q7SRY5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3TL
Query on 3TL

Download CCD File 
A
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3TLKi :  180   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.190 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.253α = 90
b = 61.253β = 90
c = 82.231γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Advisory, Refinement description