Biological Assembly 1  

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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: 22407.43 
• Atom Count: 1576 
• Residue Count: 204 
• Unique protein chains: 2

4GYE

MDR 769 HIV-1 Protease in Complex with Reduced P1F

• DOI: 10.2210/pdb4GYE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): 5 


• Deposited: 2012-09-05 Released: 2013-10-30 
• Deposition Author(s): Dewdney, T.G., Wang, Y., Brunzelle, J., Reiter, S.J., Kovari, I.A., Kovari, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.264 
• R-Value Work: 0.193 

Literature

Ligand modifications to reduce the relative resistance of multi-drug resistant HIV-1 protease.

Dewdney, T.G., Wang, Y., Liu, Z., Sharma, S.K., Reiter, S.J., Brunzelle, J.S., Kovari, I.A., Woster, P.M., Kovari, L.C.

(2013) Bioorg.Med.Chem. 21: 7430-7434

• PubMed: 24128815 
• DOI: 10.1016/j.bmc.2013.09.045
• Primary Citation of Related Structures:  
  4GZF


• PubMed Abstract: 
  

Proper proteolytic processing of the HIV-1 Gag/Pol polyprotein is required for HIV infection and viral replication. This feature has made HIV-1 protease an attractive target for antiretroviral drug design for the treatment of HIV-1 infected patients. To examine the role of the P1 and P1'positions of the substrate in inhibitory efficacy of multi-drug resistant HIV-1 protease 769 (MDR 769), we performed a series of structure-function studies. Using the original CA/p2 cleavage site sequence, we generated heptapeptides containing one reduced peptide bond with an L to F and A to F double mutation at P1 and P1' (F-r-F), and an A to F at P1' (L-r-F) resulting in P1/P1' modified ligands. Here, we present an analysis of co-crystal structures of CA/p2 F-r-F, and CA/p2 L-r-F in complex with MDR 769. To examine conformational changes in the complex structure, molecular dynamic (MD) simulations were performed with MDR769-ligand complexes. MD trajectories show the isobutyl group of both the lopinavir analog and the CA/p2 L-r-F substrate cause a conformational change of in the active site of MDR 769. IC50 measurements suggest the non identical P1/P1' ligands (CA/p2 L-r-F and lopinavir analog) are more effective against MDR proteases as opposed to identical P1/P1'ligands. Our results suggest that a non identical P1/P1'composition may be more favorable for the inhibition of MDR 769 as they induce conformational changes in the active site of the enzyme resulting in disruption of the two-fold symmetry of the protease, thus, stabilizing the inhibitor in the active site.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol
Find proteins for Q9QM22 (Human immunodeficiency virus 1) Go to UniProtKB:  Q9QM22

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
P1F peptide	C	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000778	C	N-[(2S)-2-({N~5~-[(1E)-ethanimidoyl]-L-ornithyl-L-valyl}amino)-3-phenylpropyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucine	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.264 
• R-Value Work: 0.193 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.255	α = 90.00
b = 62.255	β = 90.00
c = 83.920	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-05 
• Released Date: 2013-10-30 
• Deposition Author(s): Dewdney, T.G., Wang, Y., Brunzelle, J., Reiter, S.J., Kovari, I.A., Kovari, L.C.

Revision History 

• Version 1.0: 2013-10-30
  Type: Initial release
• Version 1.1: 2013-11-13
  Type: Database references