3E90

West Nile vi rus NS2B-NS3protease in complexed with inhibitor Naph-KKR-H

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 

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Literature

Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation

Robin, G., Chappell, K., Stoermer, M.J., Hu, S.-H., Young, P.R., Fairlie, D.P., Martin, J.L.

(2009) J Mol Biol 385: 1568-1577

  • DOI: 10.1016/j.jmb.2008.11.026
  • Primary Citation of Related Structures:  
    3E90

  • PubMed Abstract: 

    • Over the last decade, West Nile virus has spread rapidly via mosquito transmission from infected migratory birds to humans. One potential therapeutic approach to treating infection is to inhibit the virally encoded serine protease that is essential for viral replication ...

    Over the last decade, West Nile virus has spread rapidly via mosquito transmission from infected migratory birds to humans. One potential therapeutic approach to treating infection is to inhibit the virally encoded serine protease that is essential for viral replication. Here we report the crystal structure of the viral NS3 protease tethered to its essential NS2B cofactor and bound to a potent substrate-based tripeptide inhibitor, 2-naphthoyl-Lys-Lys-Arg-H (K(i)=41 nM), capped at the N-terminus by 2-naphthoyl and capped at the C-terminus by aldehyde. An important and unexpected feature of this structure is the presence of two conformations of the catalytic histidine suggesting a role for ligand stabilization of the catalytically competent His conformation. Analysis of other West Nile virus NS3 protease structures and related serine proteases supports this hypothesis, suggesting that the common catalytic mechanism involves an induced-fit mechanism.

    Organizational Affiliation: 

    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS2B cofactorA, C50West Nile virusMutation(s): 0 
Gene Names: NS2B-NS3PROTEASE
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06935
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 proteaseB, D198West Nile virusMutation(s): 0 
Gene Names: NS2B-NS3PROTEASE
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06935
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NKK
Query on NKK
Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]		N~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide
C29 H44 N8 O4
VYVVOKKLVHYYQD-SDHOMARFSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NKK BindingDB:  3E90 Ki: 41 (nM) from 1 assay(s)
IC50: 231 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.511α = 90
b = 165.915β = 90
c = 79.818γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance