7I17 | pdb_00007i17

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C10 from the F2X-Entry Screen in orthorhombic space group

• PDB DOI: https://doi.org/10.2210/pdb7I17/pdb
• Deposition Group: G_1002335 (changed state) ExploreG_1002335

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


• Deposited: 2025-02-03 Released: 2025-05-21 
• Deposition Author(s): Barthel, T., Benz, L.S., Wollenhaupt, J., Weiss, M.S.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening

Barthel, T., Wollenhaupt, J., Benz, L.S., Reincke, P., Zhang, L., Lennartz, F., Tabermann, H., Mueller, U., Meente, A., Hilgenfeld, R., Weiss, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.05 kDa 
• Atom Count: 5,275 
• Modeled Residue Count: 604 
• 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
TJV (Subject of Investigation/LOI)	D [auth A]	1,3-benzodioxole-5-carbothioamide C8 H7 N O2 S YHXXBQMLJHUUJU-UHFFFAOYSA-N
DMS	E [auth A], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.89	α = 90
b = 99.84	β = 90
c = 103.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Barthel, T., Benz, L.S., Wollenhaupt, J., Weiss, M.S.

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Funding Organization	Location	Grant Number
European Commission	European Union	871037

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release