8AZC

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

• PDB DOI: https://doi.org/10.2210/pdb8AZC/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: 0.93 Å
• R-Value Free: 0.153 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.53 kDa 
• Atom Count: 1,632 
• Modelled Residue Count: 169 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	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 P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPO (Subject of Investigation/LOI)	C [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.93 Å
• R-Value Free: 0.153 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.797	α = 90
b = 30.17	β = 96.76
c = 39.484	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
  
• Version 1.1: 2024-09-18
  Changes: Derived calculations