8ILC

Crystal structure of SetMet CoV-Y domain of Nsp3 in SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8ILC/pdb

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


• Deposited: 2023-03-03 Released: 2023-05-24 
• Deposition Author(s): Wang, K., Nan, J., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Crystal structure of SetMet CoV-Y domain of Nsp3 in SARS-CoV-2

Wang, K., Nan, J., Lei, J.

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

Macromolecule Content

• Total Structure Weight: 32.03 kDa 
• Atom Count: 2,262 
• Modelled Residue Count: 278 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	283	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.014	α = 90
b = 108.014	β = 90
c = 53.909	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXCD	phasing
SCALA	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Wang, K., Nan, J., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2021YFF0702004

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release