1DXP | pdb_00001dxp

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.298 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


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 Biological Chem 275: 7152

  • 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.

    • Organizational Affiliation: 
    • Biotechnology, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEASE/HELICASE NS3 (P70)
A, B
187Hepatitis 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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NONSTRUCTURAL PROTEIN NS4A (P4)
C, D
16Hepatitis C virus (isolate Taiwan)Mutation(s): 0 
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26662
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.298 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.98α = 90
b = 92.98β = 90
c = 81.81γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-12
    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: 2014-03-12
    Changes: Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description