5YVJ | pdb_00005yvj

Crystal structure of full length NS2B47-NS3 (gD4NS2BNS3) from Dengue virus 4 in open conformation

PDB DOI: https://doi.org/10.2210/pdb5YVJ/pdb

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

Deposited: 2017-11-26 Released: 2018-11-28
Deposition Author(s): Phoo, W.W., El Sahili, A.
Funding Organization(s): NTU, NMRC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

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., Vasudevan, S., Lescar, J., Luo, D.

To be published.

Macromolecule Content

Total Structure Weight: 74.79 kDa
Atom Count: 4,842
Modelled Residue Count: 604
Deposited Residue Count: 665
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]	618	dengue virus type 4	Mutation(s): 1
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 LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B [auth C]	47	dengue virus type 4	Mutation(s): 0
UniProt
Find proteins for Q2YHE8 (dengue virus type 4) Explore Q2YHE8 Go to UniProtKB: Q2YHE8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YHE8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 2.51 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.78	α = 90
b = 86.81	β = 93.07
c = 75.9	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: 2018-11-28

Deposition Author(s):

Funding Organization	Location	Grant Number
NTU	Singapore	START UP GRANT
NMRC	Singapore	CBRG14May05

Revision History (Full details and data files)

Version 1.0: 2018-11-28
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.