8S9Z | pdb_00008s9z

Mpro inhibitors of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8S9Z/pdb

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


• Deposited: 2023-03-30 Released: 2024-04-03 
• Deposition Author(s): Blankenship, L.R., Liu, W.R.
• Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.258 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.238 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structure of MPI89 with Mpro of SARS-CoV-2 at 1.85A resolution.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.43 kDa 
• Atom Count: 2,723 
• Modeled Residue Count: 311 
• Deposited Residue Count: 311 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mpro inhibitor	B	5	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ZU0	B	L-PEPTIDE LINKING	C8 H17 N O3		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.258 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.238 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.267	α = 90
b = 82.318	β = 96.17
c = 86.441	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Blankenship, L.R., Liu, W.R.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	A1715
Welch Foundation	United States	A-2089
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01GM138863

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Derived calculations, Structure summary