8TY3

MI-31 ligand bound to SARS-CoV-2 Mpro

• PDB DOI: https://doi.org/10.2210/pdb8TY3/pdb

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


• Deposited: 2023-08-24 Released: 2024-08-28 
• Deposition Author(s): Blankenship, L.R., Liu, W.R.
• Funding Organization(s): Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.224 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

MI-31 bound to SARS-CoV-2 Mpro

Blankenship, L.R., Liu, W.R.

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)

Macromolecule Content

• Total Structure Weight: 34.32 kDa 
• Atom Count: 2,614 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
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
SJF (Subject of Investigation/LOI)	B [auth A]	(1S,3aR,6aS)-2-[(3,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide C23 H29 Cl2 N3 O5 DSVCEMXKUZHNPU-ICWLNENESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.224 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.532	α = 90
b = 80.228	β = 96.503
c = 89.337	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Blankenship, L.R., Liu, W.R.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	A-1715
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM145351

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary