5YVV

Crystal structure of full length NS3 protein (gD4NS2BNS3) from DENV4 in closed conformation

PDB DOI: https://doi.org/10.2210/pdb5YVV/pdb

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

Deposited: 2017-11-27 Released: 2018-12-05
Deposition Author(s): PHOO, W.W., Sahili, A.E.
Funding Organization(s): NTU, NMRC, NRF

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.279
R-Value Work: 0.233
R-Value Observed: 0.235

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: 73.29 kDa
Atom Count: 4,776
Modelled Residue Count: 630
Deposited Residue Count: 655
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A [auth B]	599	dengue virus type 4	Mutation(s): 2
UniProt
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991)) Explore Q2YHF0 Go to UniProtKB: Q2YHF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YHF0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B [auth A]	56	dengue virus type 4	Mutation(s): 0
UniProt
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991)) Explore Q2YHF0 Go to UniProtKB: Q2YHF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YHF0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.279
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.917	α = 90
b = 88.715	β = 93.08
c = 81.295	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Funding Organization	Location	Grant Number
NTU	Singapore	START UP GRANT
NMRC	Singapore	CBRG14MAY051
NMRC	Singapore	CBRG/0103/2016
NRF	Singapore	CRP001-063

Revision History (Full details and data files)

Version 1.0: 2018-12-05
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.