6W9C | pdb_00006w9c

The crystal structure of papain-like protease of SARS CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6W9C/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-22 Released: 2020-04-01 
• Deposition Author(s): Osipiuk, J., Jedrzejczak, R., Tesar, C., Endres, M., Stols, L., Babnigg, G., Kim, Y., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of papain-like protease of SARS CoV-2

Osipiuk, J., Jedrzejczak, R., Tesar, C., Endres, M., Stols, L., Babnigg, G., Kim, Y., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 107.81 kDa 
• Atom Count: 7,371 
• Modeled Residue Count: 926 
• Deposited Residue Count: 951 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B, C	317	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.19.12
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B], H [auth C], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], G [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w9c

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.786	α = 90
b = 110.28	β = 96.22
c = 64.069	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Osipiuk, J., Jedrzejczak, R., Tesar, C., Endres, M., Stols, L., Babnigg, G., Kim, Y., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 2.0: 2020-05-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 3.0: 2020-10-21
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 3.1: 2021-01-27
  Changes: Structure summary
• Version 3.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description