7VH8

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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.205 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

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 of Related Structures:  
  7VH8

---

Organizational Affiliation: 

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, 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: 34.41 kDa 
• Atom Count: 2,800 
• Modelled 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 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• 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.

---

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