6DIT

Crystal structure of HCV NS3/4A protease in complex with P4-2 (JZ01-19)

• PDB DOI: https://doi.org/10.2210/pdb6DIT/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-23 Released: 2019-07-31 
• Deposition Author(s): Matthew, A.N., Schiffer, C.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

Design of Hepatitis C NS3/4A Protease Inhibitors Leveraging Untapped Regions of the Substrate Envelope

Matthew, A.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: 22.01 kDa 
• Atom Count: 1,690 
• Modelled Residue Count: 197 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease	A	199	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for A0A0B4WYC6 (Hepacivirus hominis) Explore A0A0B4WYC6  Go to UniProtKB:  A0A0B4WYC6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKJ	B [auth A]	pentyl [(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5, 16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6- yl]carbamate C38 H52 N6 O9 S XMVGSOUFSMLCKC-OJHKTYPMSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.331	α = 90
b = 58.562	β = 90
c = 59.813	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Matthew, A.N., 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	R01 AI085051
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F31 GM119345

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary