4JMY | pdb_00004jmy

Crystal structure of HCV NS3/NS4A protease complexed with DDIVPC peptide

• PDB DOI: https://doi.org/10.2210/pdb4JMY/pdb

• Classification: HYDROLASE/PROTEIN BINDING
• Organism(s): Hepatitis C virus genotype 2, Hepatitis C virus genotype 1b (isolate Japanese)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-14 Released: 2013-10-30 
• Deposition Author(s): Lemke, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.254 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Importance of the peptide scaffold of drugs that target the hepatitis C virus NS3 protease and its crucial bioactive conformation and dynamic factors.

LaPlante, S., Lemke, C.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.46 kDa 
• Atom Count: 3,146 
• Modeled Residue Count: 402 
• Deposited Residue Count: 418 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A, B	186	Hepatitis C virus genotype 2	Mutation(s): 0  Gene Names: POLG_HCVJA EC: 3.4.21.98
UniProt
Find proteins for Q81817 (Hepatitis C virus genotype 2) Explore Q81817  Go to UniProtKB:  Q81817

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV non-structural protein 4A	C, D	17	N/A	Mutation(s): 0
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
substrate peptide	E, F	6	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	H [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.254 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.123	α = 90
b = 94.123	β = 90
c = 83.236	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Lemke, C.T.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations