7HQC | pdb_00007hqc

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with CACHE3HI_1696_6

• PDB DOI: https://doi.org/10.2210/pdb7HQC/pdb
• Deposition Group: G_1002327 (changed state) ExploreG_1002327

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


• Deposited: 2024-12-08 Released: 2025-08-20 
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.153 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.140 (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: 36.77 kDa 
• Atom Count: 3,797 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BJQ (Subject of Investigation/LOI)	D [auth A]	5-ethyl-N-(4,4,4-trifluoro-2,2-dimethylbutyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine C14 H19 F3 N4 RNMNQKUTWUVHFB-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.153 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.694	α = 90
b = 88.694	β = 90
c = 39.503	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: 2025-08-20 
Deposition Author(s): Correy, G.J., Fraser, J.S.

---

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

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release