6P6V

HCV NS3/4A protease domain of genotype 5a in complex with glecaprevir

• PDB DOI: https://doi.org/10.2210/pdb6P6V/pdb

• Classification: VIRAL PROTEIN, Hydrolase
• Organism(s): Hepatitis C virus SA13
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-04 Released: 2020-06-10 
• Deposition Author(s): Timm, J., Schiffer, C.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Molecular mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir and characterization of genotype-specific structural differences

Timm, J., Kosovrasti, K., Henes, M., Leidner, F., Hou, S., Kurt-Yilmaz, N., Schiffer, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.37 kDa 
• Atom Count: 1,772 
• Modelled Residue Count: 193 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 4A,Serine protease NS3	A	203	Hepatitis C virus SA13	Mutation(s): 5  EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for O91936 (Hepatitis C virus genotype 5a (isolate SA13)) Explore O91936  Go to UniProtKB:  O91936

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O31 (Subject of Investigation/LOI)	E [auth A]	(3aR,7S,10S,12R,21E,24aR)-7-tert-butyl-N-[(1R,2R)-2-(difluoromethyl)-1-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}cyclop ropyl]-20,20-difluoro-5,8-dioxo-2,3,3a,5,6,7,8,11,12,20,23,24a-dodecahydro-1H,10H-9,12-methanocyclopenta[18,19][1,10,17, 3,6]trioxadiazacyclononadecino[11,12-b]quinoxaline-10-carboxamide C38 H46 F4 N6 O9 S MLSQGNCUYAMAHD-ITNVBOSISA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.551	α = 90
b = 60.147	β = 90
c = 83.788	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

Currently 6P6V does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Timm, J., Schiffer, C.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI085051

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary