3AV9

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: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3AVA, 3AVB, 3AVC, 3AVF, 3AVG, 3AV9, 3AVH, 3AVI, 3AVJ, 3AVK

  • 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
IntegraseAB183Human 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)
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 peptideXY8Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000817
Query on PRD_000817
X, YLEDGF peptideCyclic peptide /  Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.958α = 90
b = 70.958β = 90
c = 67.054γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2013-06-19
    Changes: Database references