7VH8 | pdb_00007vh8

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332

• PDB DOI: https://doi.org/10.2210/pdb7VH8/pdb

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


• Deposited: 2021-09-21 Released: 2021-11-03 
• Deposition Author(s): Zhao, Y., Zhang, Q., Yang, H., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332.

Zhao, Y., Fang, C., Zhang, Q., Zhang, R., Zhao, X., Duan, Y., Wang, H., Zhu, Y., Feng, L., Zhao, J., Shao, M., Yang, X., Zhang, L., Peng, C., Yang, K., Ma, D., Rao, Z., Yang, H.

(2022) Protein Cell 13: 689-693

• PubMed: 34687004 
• DOI: https://doi.org/10.1007/s13238-021-00883-2
• Primary Citation Related Structures: 
  7VH8

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, 44195, USA.
State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100091, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, Nankai University, and Tianjin Key Laboratory of Protein Sciences, Tianjin, 300071, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [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: 34.41 kDa 
• Atom Count: 2,800 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WI	B [auth A]	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C23 H34 F3 N5 O4 WDVIRQQKRMIXGS-XIFHJVQQSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.341	α = 90
b = 63.256	β = 90
c = 105.953	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Zhao, Y., Zhang, Q., Yang, H., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 2.0: 2021-12-22
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2022-07-06
  Changes: Database references
• Version 3.0: 2023-07-05
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 3.2: 2024-11-06
  Changes: Structure summary