1DY9

Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor I)

• PDB DOI: https://doi.org/10.2210/pdb1DY9/pdb

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


• Deposited: 2000-01-31 Released: 2001-01-28 
• Deposition Author(s): Di Marco, S., Rizzi, M., Volpari, C., Walsh, M., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.275 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Inhibition of the Hepatitis C Virus Ns3/4A Protease the Crystal Structures of Two Protease-Inhibitor Complexes

Di Marco, S., Rizzi, M., Volpari, C., Walsh, M., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.

(2000) J Biol Chem 275: 7152

• PubMed: 10702283 
• DOI: https://doi.org/10.1074/jbc.275.10.7152
• Primary Citation of Related Structures:  
  1DXP, 1DY8, 1DY9


• PubMed Abstract: 
  

  The hepatitis C virus NS3 protein contains a serine protease domain with a chymotrypsin-like fold, which is a target for development of therapeutics. We report the crystal structures of this domain complexed with NS4A cofactor and with two potent, reversible covalent inhibitors spanning the P1-P4 residues. Both inhibitors bind in an extended backbone conformation, forming an anti-parallel beta-sheet with one enzyme beta-strand. The P1 residue contributes most to the binding energy, whereas P2-P4 side chains are partially solvent exposed. The structures do not show notable rearrangements of the active site upon inhibitor binding. These results are significant for the development of antivirals.

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Organizational Affiliation: 

Biotechnology, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 43.96 kDa 
• Atom Count: 3,018 
• Modelled Residue Count: 374 
• Deposited Residue Count: 406 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE/HELICASE NS3 (P70)	A, B	187	Hepatitis C virus (isolate Taiwan)	Mutation(s): 0  Gene Names: HCV EC: 3.4.22
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NONSTRUCTURAL PROTEIN NS4A (P4)	C, D	16	Hepatitis C virus (isolate Taiwan)	Mutation(s): 2
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2ZF	E [auth A], F [auth B]	N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide C21 H33 F2 N3 O9 WXVMZATZAOHPFR-AVGNSLFASA-N
ZN	G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000426 (2ZF)	E [auth A], F [auth B]	BOC-GLU-LEU-FKI, PEPTIDE INHIBITOR	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.275 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.35	α = 90
b = 94.35	β = 90
c = 82.37	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-28 
Deposition Author(s): Di Marco, S., Rizzi, M., Volpari, C., Walsh, M., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.

Revision History  

• Version 1.0: 2001-01-28
  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: 2012-11-30
  Changes: Other
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-10-09
  Changes: Data collection, Other
• Version 1.5: 2023-12-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary