7IJS | pdb_00007ijs

Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group -- Crystal Structure of SARS-CoV-2 NSP3 Macrodomain in complex with POB0209 (Mac1-x10314)

• PDB DOI: https://doi.org/10.2210/pdb7IJS/pdb
• Deposition Group: G_1002351 (changed state) ExploreG_1002351

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


• Deposited: 2025-08-04 Released: 2025-08-13 
• Deposition Author(s): Aschenbrenner, J.C., Watt, G., Marples, P.G., Wang, X., Schuller, M., O'Brien, P., Fearon, D., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group

Aschenbrenner, J.C., Watt, G., Marples, P.G., Wang, X., Donald, J.R., Butler, W.T.W., Shaw, A., Schuller, M., O'Brien, P., Fearon, D., von Delft, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.92 kDa 
• Atom Count: 3,168 
• Modeled Residue Count: 335 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
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
A1CLW (Subject of Investigation/LOI)	C [auth A]	(1R,2R)-2-(1,3-benzothiazol-6-yl)cyclopentane-1-carboxylic acid C13 H13 N O2 S UQINUOHQWWOSCD-VHSXEESVSA-N
DMS	D [auth A], E [auth A], F [auth A], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.985	α = 90
b = 88.985	β = 90
c = 39.782	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Aschenbrenner, J.C., Watt, G., Marples, P.G., Wang, X., Schuller, M., O'Brien, P., Fearon, D., von Delft, F.

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release