Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.67 kDa 
• Atom Count: 5,371 
• Modelled Residue Count: 626 
• Deposited Residue Count: 636 
• Unique protein chains: 1

 7M1Y

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen

• PDB DOI:  https://doi.org/10.2210/pdb7M1Y/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-03-15 Released: 2021-03-24 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Maltseva, N., 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.213 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen

Osipiuk, J., Tesar, C., Endres, M., Maltseva, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease	A, B	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JT (Subject of Investigation/LOI)	C [auth A], S [auth B]	N-phenyl-2-selanylbenzamide C13 H11 N O Se PVPUYGNPKBMXGO-UHFFFAOYSA-N
IOD	AA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	F [auth A], V [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	BA [auth B], M [auth A], N [auth A], O [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	CA [auth B], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.213 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 6₅ 2 2
• Diffraction Data: https://doi.org/10.18430/m37m1y

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.887	α = 90
b = 114.887	β = 90
c = 252.82	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Maltseva, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

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: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references, Derived calculations, Structure summary