7Z2K

Crystal structure of SARS-CoV-2 Main Protease in orthorhombic space group p212121

• PDB DOI: https://doi.org/10.2210/pdb7Z2K/pdb

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


• Deposited: 2022-02-28 Released: 2023-03-22 
• Deposition Author(s): Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.
• Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research, Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.209 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections

Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.18 kDa 
• Atom Count: 5,633 
• Modelled Residue Count: 606 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], H [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
DMS	F [auth A], G [auth A], J [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.209 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.764	α = 90
b = 101.002	β = 90
c = 103.916	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
German Federal Ministry for Education and Research	Germany	16GW0277
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description