4B75

Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function

• PDB DOI: https://doi.org/10.2210/pdb4B75/pdb

• Classification: HYDROLASE
• Organism(s): Hepatitis C virus (isolate BK)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-16 Released: 2012-10-03 
• Deposition Author(s): Saalau-Bethell, S.M., Woodhead, A.J., Chessari, G., Carr, M.G., Coyle, J., Graham, B., Hiscock, S.D., Murray, C.W., Pathuri, P., Rich, S.J., Richardson, C.J., Williams, P.A., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.250 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Discovery of an Allosteric Mechanism for the Regulation of Hcv Ns3 Protein Function.

Saalau-Bethell, S.M., Woodhead, A.J., Chessari, G., Carr, M.G., Coyle, J., Graham, B., Hiscock, S.D., Murray, C.W., Pathuri, P., Rich, S.J., Richardson, C.J., Williams, P.A., Jhoti, H.

(2012) Nat Chem Biol 8: 920

• PubMed: 23023261 
• DOI: https://doi.org/10.1038/nchembio.1081
• Primary Citation of Related Structures:  
  4B6E, 4B6F, 4B71, 4B73, 4B74, 4B75, 4B76


• PubMed Abstract: 
  

  Here we report a highly conserved new binding site located at the interface between the protease and helicase domains of the hepatitis C virus (HCV) NS3 protein. Using a chemical lead, identified by fragment screening and structure-guided design, we demonstrate that this site has a regulatory function on the protease activity via an allosteric mechanism. We propose that compounds binding at this allosteric site inhibit the function of the NS3 protein by stabilizing an inactive conformation and thus represent a new class of direct-acting antiviral agents.

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Organizational Affiliation: 

Astex Pharmaceuticals, Cambridge Science Park, Cambridge, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 142.5 kDa 
• Atom Count: 10,059 
• Modelled Residue Count: 1,287 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NON-STRUCTURAL PROTEIN 4A, SERINE PROTEASE NS3	A, B	666	Hepatitis C virus (isolate BK)	Mutation(s): 1  EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663  Go to UniProtKB:  P26663

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4VA	C [auth A], D [auth B]	(2S)-4-amino-N-[(1R)-1-(4-chloro-2-fluoro-3-phenoxyphenyl)propyl]-4-oxobutan-2-aminium C19 H23 Cl F N2 O2 DXPCUPMRYIXTFI-BLLLJJGKSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.250 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.489	α = 90
b = 108.828	β = 90
c = 139.338	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
CSEARCH	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Saalau-Bethell, S.M., Woodhead, A.J., Chessari, G., Carr, M.G., Coyle, J., Graham, B., Hiscock, S.D., Murray, C.W., Pathuri, P., Rich, S.J., Richardson, C.J., Williams, P.A., Jhoti, H.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2012-10-31
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description