9VAO | pdb_00009vao

Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb9VAO/pdb

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


• Deposited: 2025-06-03 Released: 2025-06-18 
• Deposition Author(s): Arya, R., Ganesh, J., Prashar, V., Kumar, M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structural and functional insights into Ubl domain-mediated regulation of SARS-CoV-2 PLpro.

Arya, R., Ganesh, J., Prashar, V., Kumar, M.

(2025) Biol Direct 20: 102-102

• PubMed: 41044763 
• DOI: https://doi.org/10.1186/s13062-025-00690-3
• Primary Citation of Related Structures:  
  9VAO


• PubMed Abstract: 
  

  SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and immune evasion. It contains an N-terminal ubiquitin-like (Ubl) domain, whose involvement in enzymatic function remains poorly understood. In this study, we investigated the role of the Ubl domain in modulating the structural dynamics and catalytic efficiency of PLpro. Using molecular dynamics (MD) simulations, inhibitor binding assays, and steady-state kinetic analyses, we found that the Ubl domain stabilizes critical structural elements, notably the ridge helix in the thumb subdomain. Removal of the Ubl domain altered substrate processing, reducing catalytic efficiency of the enzyme. Interestingly, free ubiquitin enhanced enzymatic activity, likely via non-canonical binding sites distinct from the SUb1 and SUb2 sites. These findings uncover a regulatory role for the Ubl domain in allosteric modulation of PLpro activity and reveal additional layers of enzymatic plasticity. Understanding these mechanisms could guide the design of future antiviral therapeutics targeting PLpro's regulatory or allosteric sites.

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Organizational Affiliation: 
• Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India.
Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India. [e-mail].
Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India. [e-mail].
Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India. [e-mail].
Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.61 kDa 
• Atom Count: 2,920 
• Modeled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	317	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.821	α = 90
b = 81.821	β = 90
c = 133.733	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Arya, R., Ganesh, J., Prashar, V., Kumar, M.

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Funding Organization	Location	Grant Number
Other government	India	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release
  
• Version 1.1: 2025-12-31
  Changes: Database references