7GYZ | pdb_00007gyz

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0000035-001

• PDB DOI: https://doi.org/10.2210/pdb7GYZ/pdb
• Deposition Group: G_1002283 (changed state) | Explore  G_1002283  

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


• Deposited: 2024-01-23 Released: 2024-05-15 
• Deposition Author(s): Aschenbrenner, J.C., Fearon, D., Tomlinson, C.W.E., Marples, P.G., Fairhead, M., Balcomb, B.H., Chandran, A.V., Godoy, A.S., Koekemoer, L., Lithgo, R.M., Ni, X., Thompson, W., Wang, S., Wild, C., Williams, E.P., Winokan, M., Walsh, M.A., von Delft, F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.235 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the ASAP AViDD centre

Aschenbrenner, J.C., Fearon, D., Tomlinson, C.W.E., Marples, P.G., Fairhead, M., Balcomb, B.H., Chandran, A.V., Godoy, A.S., Koekemoer, L., Lithgo, R.M., Ni, X., Thompson, W., Wang, S., Wild, C., Williams, E.P., Winokan, M., Walsh, M.A., von Delft, F.

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: 3,003 
• Modeled Residue Count: 334 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
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
A1AI6	C [auth A]	N-(4-methyl-3,4-dihydro-2H-1,4-benzoxazin-5-yl)-N'-(1H-pyrazolo[3,4-b]pyridin-5-yl)urea C16 H16 N6 O2 WLZQKSBJGIMOOB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.235 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.797	α = 90
b = 88.797	β = 90
c = 39.412	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Aschenbrenner, J.C., Fearon, D., Tomlinson, C.W.E., Marples, P.G., Fairhead, M., Balcomb, B.H., Chandran, A.V., Godoy, A.S., Koekemoer, L., Lithgo, R.M., Ni, X., Thompson, W., Wang, S., Wild, C., Williams, E.P., Winokan, M., Walsh, M.A., von Delft, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171399

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release