3TRK | pdb_00003trk

Structure of the Chikungunya virus nsP2 protease

• PDB DOI: https://doi.org/10.2210/pdb3TRK/pdb

• Classification: HYDROLASE
• Organism(s): Chikungunya virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-09 Released: 2011-09-28 
• Deposition Author(s): Cheung, J., Franklin, M., Mancia, F., Rudolph, M., Cassidy, M., Gary, E., Burshteyn, F., Love, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.258 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structure of the Chikungunya virus nsP2 protease

Cheung, J., Franklin, M., Mancia, F., Rudolph, M., Cassidy, M., Gary, E., Burshteyn, F., Love, J.

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)

Macromolecule Content 

• Total Structure Weight: 37.21 kDa 
• Atom Count: 2,750 
• Modeled Residue Count: 321 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural polyprotein	A	324	Chikungunya virus	Mutation(s): 0  Gene Names: CHIKVgp1
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype)) Explore Q8JUX6  Go to UniProtKB:  Q8JUX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.258 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.509	α = 90
b = 87.509	β = 90
c = 85.078	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Cheung, J., Franklin, M., Mancia, F., Rudolph, M., Cassidy, M., Gary, E., Burshteyn, F., Love, J.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary