3AVG

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site.

Rhodes, D.I.Peat, T.S.Vandegraaff, N.Jeevarajah, D.Newman, J.Martyn, J.Coates, J.A.Ede, N.J.Rea, P.Deadman, J.J.

(2011) Chembiochem 12: 2311-2315

  • DOI: 10.1002/cbic.201100350
  • Primary Citation of Related Structures:  
    3AV9, 3AVA, 3AVB, 3AVC, 3AVF, 3AVG, 3AVH, 3AVI, 3AVJ, 3AVK, 3AVL, 3AVM, 3AVN

  • PubMed Abstract: 
  • An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site ...

    An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site. We show that the peptides inhibit the interaction of lens epithelium-derived growth factor (LEDGF) with HIV-IN in a proximity AlphaScreen assay and in an assay for the LEDGF enhancement of HIV-IN strand transfer. The interactions identified represent a potential framework for the development of new HIV-IN inhibitors.


    Organizational Affiliation

    Avexa Ltd, 576 Swan Street, Melbourne 3121, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA, B183Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 3 
Gene Names: gag-pol
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LEDGF peptideC [auth D], D [auth F]8Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.737α = 90
b = 70.737β = 90
c = 66.907γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references