7XAX | pdb_00007xax

Crystal structure of SARS coronavirus main protease in complex with Baicalei

• PDB DOI: https://doi.org/10.2210/pdb7XAX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-19 Released: 2023-03-22 
• Deposition Author(s): Zhou, X.L., Li, J., Zhang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV 3C-like protease with baicalein.

Feng, J., Li, D., Zhang, J., Yin, X., Li, J.

(2022) Biochem Biophys Res Commun 611: 190-194

• PubMed: 35490659 
• DOI: https://doi.org/10.1016/j.bbrc.2022.04.086
• Primary Citation Related Structures: 
  7XAX


• PubMed Abstract: 
  

  The 3C-like protease (M ^pro , 3CL ^pro ) plays a key role in the replication process in coronaviruses (CoVs). The M ^pro is an essential enzyme mediates CoVs replication and is a promising target for development of antiviral drugs. Until now, baicalein has been shown the specific activity for SARS-CoV M ^pro in vitro experiments. In this study, we resolved the SARS-CoV M ^pro with baicalein by X-ray diffraction at 2.25 Å (PDB code 7XAX), which provided a structural basis for the research and development of baicalein as an anti-CoVs drug.

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Organizational Affiliation: 
• Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China.
Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China; College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China. Electronic address: [e-mail].

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: 68.02 kDa 
• Atom Count: 4,435 
• Modeled Residue Count: 594 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3WL (Subject of Investigation/LOI)	C [auth A]	5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one C15 H10 O5 FXNFHKRTJBSTCS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.51	α = 90.951
b = 60.55	β = 102.715
c = 68.28	γ = 108.649

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Zhou, X.L., Li, J., Zhang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-02
  Changes: Database references
• Version 1.3: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary