3RVB | pdb_00003rvb

The structure of HCV NS3 helicase (Heli-80) bound with inhibitor ITMN-3479

PDB DOI: https://doi.org/10.2210/pdb3RVB/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Orthohepacivirus hominis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-06 Released: 2014-09-24
Deposition Author(s): Mather, O., Cheng, R., Schonfield, D., Barker, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.287 (Depositor), 0.280 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.227 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

The structure of HCV NS3 helicase with inhibitor ITMN-3479

Mather, O., Cheng, R., Schonfield, D., Barker, J.

To be published.

Macromolecule Content

Total Structure Weight: 53.37 kDa
Atom Count: 3,511
Modeled Residue Count: 443
Deposited Residue Count: 493
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA helicase	A	493	Orthohepacivirus hominis	Mutation(s): 0 Gene Names: NS3 EC: 3.6.4.13
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK)) Explore P26663 Go to UniProtKB: P26663
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26663
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I79 Query on I79 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]	{1-[(5-chloro-2-methyl-1-benzothiophen-3-yl)methyl]-6-(3,5-diaminophenyl)-1H-indol-3-yl}acetic acid C₂₆ H₂₂ Cl N₃ O₂ S PFDAXQGFXBAMGF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.287 (Depositor), 0.280 (DCC)
R-Value Work: 0.224 (Depositor), 0.220 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.354	α = 90
b = 92.354	β = 90
c = 104.462	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.