8JCO

The crystal structure of SARS-CoV-2 main protease in complex with Compound 65

• PDB DOI: https://doi.org/10.2210/pdb8JCO/pdb

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


• Deposited: 2023-05-11 Released: 2024-05-15 
• Deposition Author(s): Zhao, Y., Zhu, Y., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

The crystal structure of SARS-CoV-2 main protease in complex with Compound 65

Zhao, Y., Zhu, Y., Rao, Z.

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: 34.24 kDa 
• Atom Count: 2,717 
• Modelled Residue Count: 302 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	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
B7Y (Subject of Investigation/LOI)	B [auth A]	methyl (2S)-2-[[3-(4-chloranylbutanoyl)phenyl]carbonylamino]-3-methyl-butanoate C17 H22 Cl N O4 VVOUIVLXVGNARI-HNNXBMFYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.346	α = 90
b = 81.833	β = 114.52
c = 51.669	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Zhao, Y., Zhu, Y., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200131

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release