7FR4

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A26A - (S) isomer

• PDB DOI:  https://doi.org/10.2210/pdb7FR4/pdb
• Deposition Group: G_1002254 (changed state) ExploreG_1002254

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


• Deposited: 2022-10-20 Released: 2022-11-09 
• Deposition Author(s): Correy, G.J., Fraser, J.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.158 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

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 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: 36.77 kDa 
• Atom Count: 3,760 
• Modelled 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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
WWN (Subject of Investigation/LOI)	D [auth A]	2-cyclohexyl-N-{(2S)-1-[(7H-purin-6-yl)amino]butan-2-yl}acetamide C17 H26 N6 O DESZZRQUGKNYDX-ZDUSSCGKSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.158 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.693	α = 90
b = 88.693	β = 90
c = 39.41	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Correy, G.J., Fraser, J.S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2031205

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release