5YVW | pdb_00005yvw

Crystal structure of full length NS3 protein (eD4NS2BNS3) from DENV4 in closed conformation

PDB DOI: https://doi.org/10.2210/pdb5YVW/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., El Sahili, A.
Funding Organization(s): NTU, NMRC, NRF

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.251 (Depositor), 0.245 (DCC)
R-Value Work:
0.207 (Depositor), 0.215 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YVW

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., El Sahili, A., Zhang, Z.Z., Chen, M.W., Lescar, J., Vasudevan, S., Luo, D.

To be published.

Macromolecule Content

Total Structure Weight: 73.06 kDa
Atom Count: 4,742
Modeled Residue Count: 621
Deposited Residue Count: 646
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A [auth B]	599	dengue virus type 4	Mutation(s): 1
UniProt
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991)) Explore Q2YHF0 Go to UniProtKB: Q2YHF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YHF0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B [auth A]	47	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YHF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.251 (Depositor), 0.245 (DCC)
R-Value Work: 0.207 (Depositor), 0.215 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.77	α = 90
b = 88.3	β = 92.34
c = 81.11	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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: 2024-03-27
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.