7KYU | pdb_00007kyu

The crystal structure of SARS-CoV-2 Main Protease with the formation of Cys145-1H-indole-5-carboxylate

• PDB DOI: https://doi.org/10.2210/pdb7KYU/pdb

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


• Deposited: 2020-12-08 Released: 2020-12-16 
• Deposition Author(s): Tan, K., Maltseva, N.I., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of SARS-CoV-2 Main Protease with the formation of Cys145-1H-indole-5-carboxylate

Tan, K., Maltseva, N.I., Jedrzejczak, R.P., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 34.17 kDa 
• Atom Count: 2,577 
• Modeled 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	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b 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
XC4 (Subject of Investigation/LOI)	B [auth A]	1-[(1H-indole-5-carbonyl)oxy]-1H-benzotriazole C15 H10 N4 O2 YPFWNRLSYPAVJB-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 81.979	β = 114.634
c = 51.716	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Tan, K., Maltseva, N.I., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201 700060C

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary