9BF7 | pdb_00009bf7

SARS-CoV-2 Papain-like Protease (PLpro) C111S Untagged Crystal Structure

• PDB DOI: https://doi.org/10.2210/pdb9BF7/pdb

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


• Deposited: 2024-04-17 Released: 2025-10-01 
• Deposition Author(s): Al-Homoudi, A.I., Brunzelle, J.S., Gavande, N., Kovari, L.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Human Structural Homologues of SARS-CoV-2 PL pro as Anti-Targets: A Strategic Panel Analysis.

Al-Homoudi, A.I., Engel, J., Muczynski, M.D., Brunzelle, J.S., Gavande, N.S., Kovari, L.C.

(2025) MicroPubl Biol 2025

• PubMed: 40297819 
• DOI: https://doi.org/10.17912/micropub.biology.001418
• Primary Citation of Related Structures:  
  9BF7, 9BF8


• PubMed Abstract: 
  

  COVID-19 is caused by SARS-CoV-2, a highly transmissible and pathogenic RNA betacoronavirus. Developing small-molecule antiviral inhibitors of the SARS-CoV-2 papain-like protease (PL ^pro ) is advantageous due to the enzyme's role in processing viral polyproteins and disrupting host immune sensing. Given the structural and functional similarities between PL ^pro and human deubiquitinases (DUBs), small-molecule inhibitors are frequently counter-screened for off-target activity using a panel of human DUBs. Through X-ray crystallography, DALI structural comparisons, and in silico analysis, a high-quality crystal structure of SARS-CoV-2 PL ^pro enabled the identification of the closest structural human homologues of PL ^pro . Among the 27 human DUBs identified, USP46 and USP12 displayed the greatest structural similarity to PL ^pro , with alignment scores below 0.45 and RMSD values of 3.0 Å or less. Additionally, binding sites on ubiquitin-specific protease (USP46) and USP12, ancillary to the active site residues, share high sequence identity to the PL ^pro substrate binding sites that are often engaged by the most potent PL ^pro inhibitors. These findings offer a strong basis for choosing anti-targets and serve as a foundation for designing selective small-molecule PL ^pro inhibitors.

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Organizational Affiliation: 
• Dept. of Biochemistry, Microbiology and Immunology, Wayne State University, School of Medicine, Detroit, MI, USA.
Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, IL, USA.
Dept. of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA.
Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University, School of Medicine, Detroit, MI, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.43 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 315 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	315	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.729	α = 90
b = 81.729	β = 90
c = 134.563	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
autoPROC	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Al-Homoudi, A.I., Brunzelle, J.S., Gavande, N., Kovari, L.C.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Database references