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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 f ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS2B cofactor
A, C
50West Nile virusMutation(s): 0 
Find proteins for P06935 (West Nile virus)
Go to UniProtKB:  P06935
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS3 protease
B, D
198West Nile virusMutation(s): 0 
Find proteins for P06935 (West Nile virus)
Go to UniProtKB:  P06935
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NKK
Query on NKK

Download SDF File 
Download CCD File 
B, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NKKKi: 41 nM (96) BINDINGDB
NKKIC50: 231 nM (96) BINDINGDB
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 = 90.00
b = 165.915β = 90.00
c = 79.818γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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