8WS3

Crystal structure of SARS-CoV-2 Main Protease (Mpro) with covalent inhibitor 5,8-Dihydroxy-1,4-naphthoquinone

• PDB DOI: https://doi.org/10.2210/pdb8WS3/pdb

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


• Deposited: 2023-10-16 Released: 2024-10-23 
• Deposition Author(s): Yang, Y., Wu, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Covalent inhibitors of SARS-CoV-2 main protease

Yang, Y., Wu, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.13 kDa 
• Atom Count: 4,768 
• Modelled Residue Count: 600 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth B], B [auth A]	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X7F (Subject of Investigation/LOI)	D [auth A]	5,8-bis(oxidanyl)naphthalene-1,4-dione C10 H6 O4 RQNVIKXOOKXAJQ-UHFFFAOYSA-N
PEG	C [auth B], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.562	α = 90
b = 80.994	β = 90.17
c = 63.692	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data collection
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Yang, Y., Wu, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release