5YW1

Crystal structure of full length NS3 protein (eD4NS2BNS3) in complex with Bovine Pancreatic Trypsin Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5YW1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 4, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-28 Released: 2019-01-02 
• Deposition Author(s): Phoo, W.W., El Sahili, A.
• Funding Organization(s): National Research Foundation (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

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

Phoo, W.W., Sahili, A.E., Zhang, Z.Z., Chen, M.W., Lescar, J., Vasudevan, S., 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: 81.82 kDa 
• Atom Count: 5,277 
• Modelled Residue Count: 693 
• Deposited Residue Count: 727 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase S7	A [auth B]	618	dengue virus type 4	Mutation(s): 0
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
FLAVIVIRUS_NS2B	B [auth A]	54	dengue virus type 4	Mutation(s): 0
UniProt
Find proteins for W0LLP9 (dengue virus type 4) Explore W0LLP9  Go to UniProtKB:  W0LLP9

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.018	α = 90
b = 87.493	β = 98.25
c = 86.455	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Phoo, W.W., El Sahili, A.

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Funding Organization	Location	Grant Number
	Singapore	START UP GRANT
	Singapore	CBRG14MAY051
	Singapore	CBRG/0103/2016
National Research Foundation (Singapore)	Singapore	CRP001-063

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary