Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43005.64 
• Atom Count: 2688 
• Residue Count: 382 
• Unique protein chains: 2

3AVI

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

• DOI: 10.2210/pdb3AVI/pdb

• Classification: RECOMBINATION/INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2011-03-05 Released: 2012-02-15 
• Deposition Author(s): Peat, T.S., Deadman, J.J., Newman, J., Rhodes, D.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 

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

• PubMed: 21850718 
• DOI: 10.1002/cbic.201100350
• Primary Citation of Related Structures:  
  3AVN, 3AVM, 3AVL, 3AVK, 3AVJ, 3AVH, 3AVG, 3AVF, 3AVC, 3AVB, 3AVA, 3AV9


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Integrase	A, B	183	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)	Mutation(s): 3  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
LEDGF peptide	D, F	8	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
ACY	A, B	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000821	D,F	SLKIDNMD peptide	Cyclic peptide / Enzyme inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 
• Space Group: P 3₁

Unit Cell:

Length (Å)	Angle (°)
a = 70.995	α = 90.00
b = 70.995	β = 90.00
c = 66.996	γ = 120.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-05 
• Released Date: 2012-02-15 
• Deposition Author(s): Peat, T.S., Deadman, J.J., Newman, J., Rhodes, D.I.

Revision History 

• Version 1.0: 2012-02-15
  Type: Initial release
• Version 1.1: 2012-12-12
  Type: Other
• Version 1.2: 2013-06-19
  Type: Database references