6DIR | pdb_00006dir

Crystal structure of HCV NS3/4A protease in complex with P4-P5-2 (AJ-67)

• PDB DOI: https://doi.org/10.2210/pdb6DIR/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: 1.75 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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: 22.24 kDa 
• Atom Count: 1,769 
• Modeled Residue Count: 198 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKA (Subject of Investigation/LOI)	B [auth A]	(2R,6S,12Z,13aS,14aR,16aS)-6-[(N-acetyl-3-methyl-L-valyl)amino]-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-N-[(1-methyl cyclopropyl)sulfonyl]-5,16-dioxo-1,2,3,6,7,8,9,10,11,13a,14,15,16,16a-tetradecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diaz acyclopentadecine-14a(5H)-carboxamide C40 H55 N7 O9 S YOHPIODWEANJQZ-UYLSUIKTSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.147	α = 90
b = 59.81	β = 90
c = 58.465	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