7D47 | pdb_00007d47

Crystal structure of SARS-CoV-2 Papain-like protease C111S

• PDB DOI: https://doi.org/10.2210/pdb7D47/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2020-09-22 Released: 2020-10-07 
• Deposition Author(s): Wu, K.-P., Chen, S.-K., Lu, Y.-C., Huang, Y.-C.J., Lee, M.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 Papain-like protease

Wu, K.-P., Chen, S.-K., Lu, Y.-C., Huang, Y.-C.J., Lee, M.-H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.91 kDa 
• Atom Count: 5,142 
• Modeled Residue Count: 617 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	317	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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 (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.846	α = 90
b = 110.846	β = 90
c = 66.22	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Wu, K.-P., Chen, S.-K., Lu, Y.-C., Huang, Y.-C.J., Lee, M.-H.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description