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: 37.67 kDa 
• Atom Count: 2,774 
• Modelled Residue Count: 325 
• Deposited Residue Count: 331 
• Unique protein chains: 2

 6WX4

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR251

• PDB DOI:  https://doi.org/10.2210/pdb6WX4/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2, saltans group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-09 Released: 2020-05-20 
• Deposition Author(s): Lv, Z., Olsen, S.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.

Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S.J., El Oualid, F., Huang, T.T., Bekes, M., Drag, M., Olsen, S.K.

(2020) Sci Adv 6

• PubMed: 33067239 
• DOI: https://doi.org/10.1126/sciadv.abd4596
• Primary Citation of Related Structures:  
  6WUU, 6WX4


• PubMed Abstract: 
  

Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.

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Related Citations: 

• Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design.
  Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S.J., El Oualid, F., Huang, T.T., Bekes, M., Drag, M., Olsen, S.K.
  (2020) Biorxiv --: --

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Organizational Affiliation: 

Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A [auth D]	326	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VIR251	B [auth I]	5	saltans group	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
73O	B [auth I]	L-PEPTIDE LINKING	C10 H13 N O3		TYR
DPP	B [auth I]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002390	B [auth I]	Papain-like protease peptide inhibitor VIR251	Peptide-like / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.869	α = 90
b = 113.482	β = 90
c = 151.048	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Lv, Z., Olsen, S.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115568-05

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 1.2: 2020-12-02
  Changes: Database references, Derived calculations
• Version 1.3: 2021-01-27
  Changes: Structure summary