3KF2 | pdb_00003kf2

The HCV NS3/NS4A protease apo structure

• PDB DOI: https://doi.org/10.2210/pdb3KF2/pdb

• Classification: HYDROLASE
• Organism(s): Orthohepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-10-27 Released: 2010-03-09 
• Deposition Author(s): Lindberg, J.D., Nystrom, S., Cummings, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target

Cummings, M.D., Lindberg, J.D., Lin, T.-I., de Kock, H., Lenz, O., Lilja, E., Fellander, S., Baraznenok, V., Nystrom, S., Nilsson, M., Vrang, L., Edlund, M., Rosenquist, A., Samuelsson, B., Raboisson, P., Simmen, K.

(2010) Angew Chem Int Ed Engl 49: 1652-1655

• PubMed: 20166108 
• DOI: https://doi.org/10.1002/anie.200906696
• Primary Citation Related Structures: 
  3KEE, 3KF2

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Organizational Affiliation: 
• Tibotec BVBA, Gen De Wittelaan L 11B 3, 2800 Mechelen, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content 

• Total Structure Weight: 47.39 kDa 
• Atom Count: 2,782 
• Modeled Residue Count: 372 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A, C [auth B]	200	Orthohepacivirus hominis	Mutation(s): 1  EC: 3.4.21.98
UniProt
Find proteins for B2Y2M9 (Hepacivirus hominis) Explore B2Y2M9  Go to UniProtKB:  B2Y2M9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19-mer peptide from Genome polyprotein	B [auth C], D	23	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for Q6GYR8 (Hepacivirus hominis) Explore Q6GYR8  Go to UniProtKB:  Q6GYR8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.924	α = 90
b = 224.924	β = 90
c = 75.545	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Lindberg, J.D., Nystrom, S., Cummings, M.D.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description