2FP7

West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus.

Erbel, P.Schiering, N.D'Arcy, A.Renatus, M.Kroemer, M.Lim, S.P.Yin, Z.Keller, T.H.Vasudevan, S.G.Hommel, U.

(2006) Nat Struct Mol Biol 13: 372-373

  • DOI: 10.1038/nsmb1073
  • Primary Citation of Related Structures:  
    2FOM, 2FP7

  • PubMed Abstract: 
  • The replication of flaviviruses requires the correct processing of their polyprotein by the viral NS3 protease (NS3pro). Essential for the activation of NS3pro is a 47-residue region of NS2B. Here we report the crystal structures of a dengue NS2B-NS3pro complex and a West Nile virus NS2B-NS3pro complex with a substrate-based inhibitor ...

    The replication of flaviviruses requires the correct processing of their polyprotein by the viral NS3 protease (NS3pro). Essential for the activation of NS3pro is a 47-residue region of NS2B. Here we report the crystal structures of a dengue NS2B-NS3pro complex and a West Nile virus NS2B-NS3pro complex with a substrate-based inhibitor. These structures identify key residues for NS3pro substrate recognition and clarify the mechanism of NS3pro activation.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Protease Platform, 4002 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA54West Nile virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinB172West Nile virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamideC5synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
CL-PEPTIDE LINKINGC6 H13 N O2LEU
OAR
Query on OAR
CPEPTIDE-LIKEC6 H16 N4 OARG
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.425α = 90
b = 93.425β = 90
c = 47.435γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2011-11-02
    Changes: Structure summary
  • Version 1.4: 2013-02-27
    Changes: Other
  • Version 1.5: 2017-06-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.6: 2017-10-18
    Changes: Refinement description
  • Version 1.7: 2018-02-14
    Changes: Experimental preparation