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: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.183 

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:  2P3A, 2P3B, 2P3C

  • 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pol protein
A, B
99Human immunodeficiency virus 1Gene Names: pol
Find proteins for Q7SRY5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q7SRY5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3TL
Query on 3TL

Download SDF File 
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
TL-3, C2 symmetric inhibitor
C50 H64 N6 O10
BJJPNOGMLLUCER-KUTQPOQPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000434 (3TL)
Query on PRD_000434
AN-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamidePeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3TLKi: 180 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.183 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 61.253α = 90.00
b = 61.253β = 90.00
c = 82.231γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CCP4data scaling
MAR345data collection
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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