9BF8 | pdb_00009bf8

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

• PDB DOI: https://doi.org/10.2210/pdb9BF8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-17 Released: 2025-05-07 
• Deposition Author(s): Al-Homoudi, A.I., Engel, J., 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: 1.85 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.178 (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:  
  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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.89 kDa 
• Atom Count: 2,899 
• Modeled Residue Count: 315 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a polyprotein	A	315	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: ORF1ab
UniProt
Find proteins for A0A859GWA9 (Severe acute respiratory syndrome coronavirus 2) Explore A0A859GWA9  Go to UniProtKB:  A0A859GWA9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.342	α = 90
b = 82.342	β = 90
c = 136.407	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: 2025-05-07 
Deposition Author(s): Al-Homoudi, A.I., Engel, J., 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: 2025-05-07
  Type: Initial release