7TOB

Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376

• PDB DOI: https://doi.org/10.2210/pdb7TOB/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2022-01-24 Released: 2022-02-02 
• Deposition Author(s): Sacco, M.D., Wang, J., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.213 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition.

Sacco, M.D., Hu, Y., Gongora, M.V., Meilleur, F., Kemp, M.T., Zhang, X., Wang, J., Chen, Y.

(2022) Cell Res 32: 498-500

• PubMed: 35292745 
• DOI: https://doi.org/10.1038/s41422-022-00640-y
• Primary Citation of Related Structures:  
  7TOB

---

Organizational Affiliation: 

Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.

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: 34.56 kDa 
• Atom Count: 2,613 
• 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 nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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
K36 (Subject of Investigation/LOI)	B [auth A]	(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C21 H31 N3 O8 S BSPZFJDYQHDZNR-HTCLRFROSA-N
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002495 (K36)	B [auth A]	GC376	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.213 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.186	α = 90
b = 52.987	β = 100.5
c = 113.006	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Sacco, M.D., Wang, J., Chen, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158775
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147325
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI157046

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2022-05-18
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary