Biological Assembly 1  

 3D View: Structure | 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: 22.44 kDa 
• Atom Count: 1930 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

3OXC

Wild Type HIV-1 Protease with Antiviral Drug Saquinavir

• DOI: 10.2210/pdb3OXC/pdb
• Entry: 3OXC supersedes: 2NMW

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


• Deposited: 2010-09-21 Released: 2010-11-10 
• Deposition Author(s): Kovalevsky, A.Y., Wang, Y.-F., Tie, Y., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.178 
• R-Value Work: 0.137 
• R-Value Observed: 0.137 

Literature

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

Kovalevsky, A.Y., Wang, Y.-F., Tie, Y., Weber, I.T.

(2007) Proteins 67: 232-242

• PubMed: 17243183 
• DOI: 10.1002/prot.21304
• Primary Citation of Related Structures:  
  2NMY, 2NMZ, 2NNK, 2NNP, 3OXC


• PubMed Abstract: 
  

Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PR(I) (84V) and PR(V) (82A) containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors. Atomic resolution crystal structures (0.97-1.25 A) of the SQV complexes were analyzed in comparison to the protease complexes with darunavir, a new drug that targets resistant HIV, in order to understand the molecular basis of drug resistance. PR(I) (84V) and PR(V) (82A) complexes were obtained in both the space groups P2(1)2(1)2 and P2(1)2(1)2(1), which provided experimental limits for the conformational flexibility. The SQV interactions with PR were very similar in the mutant complexes, consistent with the similar inhibition constants. The mutation from bigger to smaller amino acids allows more space to accommodate the large group at P1' of SQV, unlike the reduced interactions observed in darunavir complexes. The residues 79-82 have adjusted to accommodate the large hydrophobic groups of SQV, suggesting that these residues are intrinsically flexible and their conformation depends more on the nature of the inhibitor than on the mutations in this region. This analysis will assist with development of more effective antiviral inhibitors.

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Related Citations: 

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Organizational Affiliation: 

Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA.

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 EC: 3.4.23.16
UniProt
Find proteins for Q7SSI0 (Human immunodeficiency virus 1) Explore Q7SSI0  Go to UniProtKB:  Q7SSI0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ROC (Subject of Investigation/LOI)	C [auth A]	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N
SO4	E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FMT	D [auth A], F [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ROC	BindingDB:  3OXC	Ki: min: 0.04, max: 138 (nM) from 29 assay(s)
		Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
		IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
		-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 47 assay(s)
		ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 47 assay(s)
		ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s)
	PDBBind:  3OXC	Ki: 3.9 (nM) from 1 assay(s)
	Binding MOAD:  3OXC	Ki: 3.9 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	C [auth A]	Saquinavir	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 0.178 
• R-Value Work: 0.137 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.1	α = 90
b = 59.78	β = 90
c = 62.49	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-09-21 
• Released Date: 2010-11-10 
Deposition Author(s): Kovalevsky, A.Y., Wang, Y.-F., Tie, Y., Weber, I.T.
• This entry supersedes: 2NMW

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other