5YVU | pdb_00005yvu

Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain

• PDB DOI: https://doi.org/10.2210/pdb5YVU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 4, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-11-27 Released: 2018-11-28 
• Deposition Author(s): Phoo, W.W., El Sahili, A.
• Funding Organization(s): NTU, NMRC, NRF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.266 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of unlinked full length NS3 from Dengue virus provide insights into dynamics of protease domain

Phoo, W.W., El Sahili, A., ZHANG, Z.Z., CHEN, M.W., VASUDEVAN, S., LESCAR, J., LUO, D.

To be published.

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: 82.44 kDa 
• Atom Count: 5,350 
• Modeled Residue Count: 694 
• Deposited Residue Count: 737 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A [auth B]	627	dengue virus type 4	Mutation(s): 1
UniProt
Find proteins for F8TEL4 (Dengue virus type 4) Explore F8TEL4  Go to UniProtKB:  F8TEL4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B [auth A]	55	dengue virus type 4	Mutation(s): 0
UniProt
Find proteins for F8TEL4 (Dengue virus type 4) Explore F8TEL4  Go to UniProtKB:  F8TEL4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic trypsin inhibitor	C [auth I]	55	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P00974 (Bos taurus) Explore P00974  Go to UniProtKB:  P00974

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.266 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.059	α = 90
b = 85.627	β = 97.95
c = 85.508	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Phoo, W.W., El Sahili, A.

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Funding Organization	Location	Grant Number
NTU	Singapore	STARTUP_GRANT
NMRC	Singapore	CBRG14051
NMRC	Singapore	CBRG/0103/2016
NRF	Singapore	NRF-CRP001-063

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary