2FP7

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

• PDB DOI: https://doi.org/10.2210/pdb2FP7/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): West Nile virus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-16 Released: 2006-03-07 
• Deposition Author(s): Schiering, N., D'Arcy, A., Erbel, P.

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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 

Starting Model: experimental

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

• PubMed: 16532006 
• DOI: https://doi.org/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. These structures identify key residues for NS3pro substrate recognition and clarify the mechanism of NS3pro activation.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.35 kDa 
• Atom Count: 1,619 
• Modelled Residue Count: 192 
• Deposited Residue Count: 231 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	54	West Nile virus	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B	172	West Nile virus	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-argininamide	C	5	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	C	L-PEPTIDE LINKING	C6 H13 N O2		LEU
OAR	C	PEPTIDE-LIKE	C6 H16 N4 O		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000988	C	N-benzoyl-L-norleucyl-6-ammonio-L-norleucyl-N~5~-[amino(iminio)methyl]-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-ornithinamide	Peptide-like / Inhibitor

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 = 93.425	α = 90
b = 93.425	β = 90
c = 47.435	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Schiering, N., D'Arcy, A., Erbel, P.

Revision History  

• 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
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-04-03
  Changes: Refinement description