7NTT | pdb_00007ntt

Crystal structure of the SARS-CoV-2 Main Protease

• PDB DOI: https://doi.org/10.2210/pdb7NTT/pdb

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


• Deposited: 2021-03-10 Released: 2022-03-02 
• Deposition Author(s): Dupre, E., Villeret, V., Hanoulle, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the SARS-CoV-2 Main Protease

Dupre, E., Villeret, V., Hanoulle, X.

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: 67.77 kDa 
• Atom Count: 5,060 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	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
FMT	D [auth B], E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.76	α = 90
b = 53.98	β = 101.18
c = 114.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing
XDS	data processing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Dupre, E., Villeret, V., Hanoulle, X.

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description