6P6S | pdb_00006p6s

HCV NS3/4A protease domain of genotype 3a in complex with glecaprevir

• PDB DOI: https://doi.org/10.2210/pdb6P6S/pdb

• Classification: VIRAL PROTEIN, Hydrolase
• Organism(s): Hepatitis C virus (isolate NZL1)
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

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: 22.27 kDa 
• Atom Count: 1,571 
• Modeled Residue Count: 192 
• 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 (isolate NZL1)	Mutation(s): 9  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 Q81258 (Hepatitis C virus genotype 3a (isolate NZL1)) Explore Q81258  Go to UniProtKB:  Q81258

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O31 (Subject of Investigation/LOI)	B [auth A]	Glecaprevir C38 H46 F4 N6 O9 S MLSQGNCUYAMAHD-ITNVBOSISA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.487	α = 90
b = 36.487	β = 90
c = 267.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

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
• Version 1.2: 2025-01-29
  Changes: Derived calculations, Structure summary