Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 22.46 kDa 
• Atom Count: 1821 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

3GGU

HIV PR drug resistant patient's variant in complex with darunavir

• PDB DOI: 10.2210/pdb3GGU/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-02 Released: 2009-08-11 
• Deposition Author(s): Saskova, K.G., Brynda, J., Rezacova, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir.

Saskova, K.G., Kozisek, M., Rezacova, P., Brynda, J., Yashina, T., Kagan, R.M., Konvalinka, J.

(2009) J Virol 83: 8810-8818

• PubMed: 19535439 
• DOI: 10.1128/JVI.00451-09
• Primary Citation of Related Structures:  
  3GGU, 3U7S


• PubMed Abstract: 
  

Darunavir is the most recently approved human immunodeficiency virus (HIV) protease (PR) inhibitor (PI) and is active against many HIV type 1 PR variants resistant to earlier-generation PIs. Darunavir shows a high genetic barrier to resistance development, and virus strains with lower sensitivity to darunavir have a higher number of PI resistance-associated mutations than viruses resistant to other PIs. In this work, we have enzymologically and structurally characterized a number of highly mutated clinically derived PRs with high levels of phenotypic resistance to darunavir. With 18 to 21 amino acid residue changes, the PR variants studied in this work are the most highly mutated HIV PR species ever studied by means of enzyme kinetics and X-ray crystallography. The recombinant proteins showed major defects in substrate binding, while the substrate turnover was less affected. Remarkably, the overall catalytic efficiency of the recombinant PRs (5% that of the wild-type enzyme) is still sufficient to support polyprotein processing and particle maturation in the corresponding viruses. The X-ray structures of drug-resistant PRs complexed with darunavir suggest that the impaired inhibitor binding could be explained by change in the PR-inhibitor hydrogen bond pattern in the P2' binding pocket due to a substantial shift of the aminophenyl moiety of the inhibitor. Recombinant virus phenotypic characterization, enzyme kinetics, and X-ray structural analysis thus help to explain darunavir resistance development in HIV-positive patients.

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Organizational Affiliation: 

Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, v.v.i., Flemingovo n. 2, 166 10 Prague 6, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 20  Gene Names: gag-pol, pol EC: 3.4.23.16 (PDB Primary Data), 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)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	C [auth B]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
017	Binding MOAD:  3GGU	Ki: 0.17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.593	α = 90
b = 62.593	β = 90
c = 81.923	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-02 
• Released Date: 2009-08-11 
Deposition Author(s): Saskova, K.G., Brynda, J., Rezacova, P.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary