2ZJO | pdb_00002zjo

Crystal structure of hepatitis C virus NS3 helicase with a novel inhibitor

PDB DOI: https://doi.org/10.2210/pdb2ZJO/pdb

Classification: HYDROLASE
Organism(s): Hepatitis C virus (isolate Taiwan)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-07 Released: 2009-03-10
Deposition Author(s): Liaw, S.H., Chen, S.J., Hu, C.Y., Chi, W.K., Chu, I.D., Hwang, L.H., Chern, J.W., Chen, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.287 (Depositor), 0.277 (DCC)
R-Value Work:
0.230 (Depositor), 0.228 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-Based Discovery of Triphenylmethane Derivatives as Novel Inhibitors of Hepatitis C Virus Helicase

Liaw, S.H., Chen, S.J., Hu, C.Y., Chi, W.K., Chu, I.D., Hwang, L.H., Chern, J.W., Chen, D.S.

To be published.

Macromolecule Content

Total Structure Weight: 52.63 kDa
Atom Count: 3,457
Modeled Residue Count: 444
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	482	Hepatitis C virus (isolate Taiwan)	Mutation(s): 0 EC: 3.4.21.98
UniProt
Find proteins for P29846 (Hepatitis C virus genotype 1b (isolate Taiwan)) Explore P29846 Go to UniProtKB: P29846
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29846
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BHT Query on BHT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[4-(BIS{4-[(3-SULFOPHENYL)AMINO]PHENYL}METHYLENE)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-4-SULFOBENZENAMINIUM C₃₇ H₃₀ N₃ O₉ S₃ QEJOESQJOWWNSS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.287 (Depositor), 0.277 (DCC)
R-Value Work: 0.230 (Depositor), 0.228 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.063	α = 90
b = 92.063	β = 90
c = 104.71	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.