8AZD

Structure of SARS-CoV-2 NSP3 macrodomain in complex with ADPR

• PDB DOI: https://doi.org/10.2210/pdb8AZD/pdb

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


• Deposited: 2022-09-05 Released: 2023-09-13 
• Deposition Author(s): Sander, S., Tidow, H., Fliegert, R., Sandmann, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Structure of SARS-CoV-2 NSP3 macrodomain in the apo form

Sander, S., Tidow, H., Fliegert, R., Sandmann, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.68 kDa 
• Atom Count: 2,893 
• Modelled Residue Count: 344 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	179	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
APR (Subject of Investigation/LOI)	C [auth A], D [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.534	α = 90
b = 76.01	β = 90
c = 82.848	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Sander, S., Tidow, H., Fliegert, R., Sandmann, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1328

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release