7CA8 | pdb_00007ca8

The crystal structure of COVID-19 main protease in complex with an inhibitor Shikonin

• PDB DOI: https://doi.org/10.2210/pdb7CA8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2021-04-07 
• Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Li, J., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode.

Li, J., Zhou, X., Zhang, Y., Zhong, F., Lin, C., McCormick, P.J., Jiang, F., Luo, J., Zhou, H., Wang, Q., Fu, Y., Duan, J., Zhang, J.

(2021) Sci Bull (Beijing) 66: 661-663

• PubMed: 33163253 
• DOI: https://doi.org/10.1016/j.scib.2020.10.018
• Primary Citation Related Structures: 
  7CA8

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Organizational Affiliation: 
• College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.
The Second Affiliated Hospital of Nanchang University, Nanchang 330031, China.
Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.
Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.
Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China.
William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
Human Aging Research Institute (HARI), School of Life Sciences, Nanchang University, Nanchang 330031, China.

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: 66.24 kDa 
• Atom Count: 4,250 
• Modeled Residue Count: 569 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	298	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), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNO	C [auth A]	2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione C16 H16 O5 NEZONWMXZKDMKF-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.96	α = 90
b = 102.37	β = 90
c = 103.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Li, J., Zhang, J.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description