8FWO | pdb_00008fwo

Crystal structure of SARS-CoV-2 papain-like protease

• PDB DOI: https://doi.org/10.2210/pdb8FWO/pdb

• Classification: Viral protein, HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-23 Released: 2024-01-31 
• Deposition Author(s): Bezerra, E.H.S., Soprano, A.S., Tonoli, C.C.C., Prado, P.F.V., da Silva, J.C., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 papain-like protease

Bezerra, E.H.S., Soprano, A.S., Tonoli, C.C.C., Prado, P.F.V., da Silva, J.C., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.

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: 37.32 kDa 
• Atom Count: 2,781 
• Modeled Residue Count: 311 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	324	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.005	α = 90
b = 83.005	β = 90
c = 133.964	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Bezerra, E.H.S., Soprano, A.S., Tonoli, C.C.C., Prado, P.F.V., da Silva, J.C., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.

---

Funding Organization	Location	Grant Number
Other government		01.20.0003.00
Other government		--
Other government		--

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary