1DXW

structure of hetero complex of non structural protein (NS) of hepatitis C virus (HCV) and synthetic peptidic compound


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibitor Binding Induces Active Site Stabilisation of the Hcv Ns3 Protein Serine Protease Domain

Barbato, G.Cicero, D.O.Cordier, F.Narjes, F.Gerlach, B.Sambucini, S.Grzesiek, S.Matassa, V.G.Defrancesco, R.Bazzo, R.

(2000) EMBO J 19: 1195

  • DOI: 10.1093/emboj/19.6.1195
  • Primary Citation of Related Structures:  
    1DXW

  • PubMed Abstract: 
  • Few structures of viral serine proteases, those encoded by the Sindbis and Semliki Forest viruses, hepatitis C virus (HCV) and cytomegalovirus, have been reported. In the life cycle of HCV a crucial role is played by a chymotrypsin-like serine protea ...

    Few structures of viral serine proteases, those encoded by the Sindbis and Semliki Forest viruses, hepatitis C virus (HCV) and cytomegalovirus, have been reported. In the life cycle of HCV a crucial role is played by a chymotrypsin-like serine protease encoded at the N-terminus of the viral NS3 protein, the solution structure of which we present here complexed with a covalently bound reversible inhibitor. Unexpectedly, the residue in the P2 position of the inhibitor induces an effective stabilization of the catalytic His-Asp hydrogen bond, by shielding that region of the protease from the solvent. This interaction appears crucial in the activation of the enzyme catalytic machinery and represents an unprecedented observation for this family of enzymes. Our data suggest that natural substrates of this serine protease could contribute to the enzyme activation by a similar induced-fit mechanism. The high degree of similarity at the His-Asp catalytic site region between HCV NS3 and other viral serine proteases suggests that this behaviour could be a more general feature for this category of viral enzymes.


    Related Citations: 
    • The Solution Structure of the N-Terminal Serine Protease Domain of the Hepatitis C Virus Ns3 Protein Provides New Insights Into its Activation and Catalytic Mechanism
      Barbato, G., Cicero, D.O., Nardi, M.C., Steinkuhler, C., Cortese, R., Defrancesco, R., Bazzo, R.
      (1999) J Mol Biol 289: 371
    • Structural Characterization of the Interactions of Optimized Product Inhibitors with the N-Terminal Proteinase Domain of the Hepatitis C Virus (Hcv) Ns3 Protein by NMR and Modelling Studies
      Cicero, D.O., Barbato, G., Koch, U., Ingallinella, P., Bianchi, E., Nardi, M.C., Steinkuhler, C., Cortese, R., Matassa, V., Defrancesco, R., Pessi, A., Bazzo, R.
      (1999) J Mol Biol 289: 385
    • The Metal Binding Site of the Hepatitis C Virus Ns3 Protease
      Urbani, A., Bazzo, R., Nardi, M.C., Cicero, D.O., Defrancesco, R., Steinkuhler, C., Barbato, G.
      (1998) J Biol Chem 273: 18760

    Organizational Affiliation

    Department of Biochemistry, IRBM 'P.Angeletti', Via Pontina km 30. 600, 00040 Pomezia, Roma, Italy. Barbato@irbm.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PROTEASEA186Hepacivirus CMutation(s): 0 
Find proteins for Q8QW30 (Hepatitis C virus subtype 1b)
Explore Q8QW30 
Go to UniProtKB:  Q8QW30
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2ZF
Query on 2ZF

Download CCD File 
A
N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
C21 H33 F2 N3 O9
WXVMZATZAOHPFR-AVGNSLFASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2ZFIC50:  330   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000426 (2ZF)
Query on PRD_000426
ABOC-GLU-LEU-FKI, PEPTIDE INHIBITORPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • OLDERADO: 1DXW Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: 2012-11-30
    Changes: Other
  • Version 1.3: 2020-01-15
    Changes: Data collection, Derived calculations, Other