4GYE | pdb_00004gye

MDR 769 HIV-1 Protease in Complex with Reduced P1F

• PDB DOI: https://doi.org/10.2210/pdb4GYE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.bmc.2013.09.045
• Primary Citation Related Structures: 
  4GYE, 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.41 kDa 
• Atom Count: 1,687 
• Modeled Residue Count: 204 
• Deposited Residue Count: 204 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P1F peptide	C	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	C	L-PEPTIDE LINKING	C6 H13 N O2		LEU
PUK	C	PEPTIDE-LIKE	C18 H22 N2 O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
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 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.255	α = 90
b = 62.255	β = 90
c = 83.92	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 2.0: 2023-02-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Refinement description
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 3.1: 2024-11-27
  Changes: Structure summary