7IJK | pdb_00007ijk

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990919048

• PDB DOI: https://doi.org/10.2210/pdb7IJK/pdb
• Deposition Group: G_1002350 (changed state) ExploreG_1002350

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


• Deposited: 2025-07-22 Released: 2025-09-17 
• Deposition Author(s): Correy, G.J., Fraser, J.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.153 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Ligand screen against SARS-CoV-2 NSP3 macrodomain

Correy, G.J., Fraser, J.S.

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: 36.68 kDa 
• Atom Count: 3,732 
• Modeled Residue Count: 336 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CKJ (Subject of Investigation/LOI)	C [auth A]	(2R,3S)-2-hydroxy-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid C16 H14 N4 O4 CFFIXNXNTHRLJK-WCQYABFASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.153 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.687	α = 90
b = 88.687	β = 90
c = 39.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Correy, G.J., Fraser, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110
National Institutes of Health/Office of the Director	United States	AY1AX000035

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release