3AVK | pdb_00003avk

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

• PDB DOI: https://doi.org/10.2210/pdb3AVK/pdb

• Classification: RECOMBINATION/INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE), Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-03-05 Released: 2012-01-18 
• 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: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.159 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

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: https://doi.org/10.1002/cbic.201100350
• Primary Citation 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. 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 42.92 kDa 
• Atom Count: 2,845 
• Modeled Residue Count: 314 
• Deposited Residue Count: 382 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	183	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 3  Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LEDGF peptide	C [auth D], D [auth F]	8	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	I [auth A], O [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	J [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000824	C [auth D], D [auth F]	SLKIDNED peptide	Cyclic peptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.159 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.743	α = 90
b = 70.743	β = 90
c = 66.609	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Peat, T.S., Deadman, J.J., Newman, J., Rhodes, D.I.

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
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary