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)

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8TEL4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W0LLP9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00974
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-02

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2019-01-02
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.