28BC | pdb_000028bc

Crystal structure of SARS-CoV-2 Papain-Like protease (PLpro) C111S mutant with active-site phosphate

• PDB DOI: https://doi.org/10.2210/pdb28BC/pdb

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


• Deposited: 2026-06-19 Released: 2026-07-01 
• 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: 1.92 Å
• R-Value Free: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 Papain-Like protease (PLpro) C111S mutant with active-site phosphate

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

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

Macromolecule Content 

• Total Structure Weight: 36.45 kDa 
• Atom Count: 3,037 
• 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): 1  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.998	α = 90
b = 81.998	β = 90
c = 134.893	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
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: 2026-07-01
  Type: Initial release