Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
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: 34.86 kDa 
• Atom Count: 2302 
• Modelled Residue Count: 303 
• Deposited Residue Count: 313 
• Unique protein chains: 1

8CZU

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d

• PDB DOI: 10.2210/pdb8CZU/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-05-25 Released: 2022-06-22 
• Deposition Author(s): Liu, L., Lovell, S., Battaile, K.P., Nguyen, H.N., Chamandi, S.D., Picard, H.R., Madden, T.K., Thruman, H.A., Kim, Y., Groutas, W.C., Chang, K.O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d

Chamandi, S.D., Nguyen, H.N., Rathnayake, A.D., Kim, Y., Perera, K.D., Picard, H.R., Madden, T., Thurman, H.A., Kashipathy, M.M., Liu, L., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	313	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: orf1a EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt)
UniProt
Find proteins for A0A1L2E0X0 (Middle East respiratory syndrome-related coronavirus) Explore A0A1L2E0X0  Go to UniProtKB:  A0A1L2E0X0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P9R (Subject of Investigation/LOI)	B [auth A]	[(1~{S},2~{S})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate C25 H42 N3 O8 S UNYDBHQZGVQZAY-KAXVZBFOSA-P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.443	α = 90
b = 57.312	β = 112.21
c = 49.682	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2022-05-25 
• Released Date: 2022-06-22 
Deposition Author(s): Liu, L., Lovell, S., Battaile, K.P., Nguyen, H.N., Chamandi, S.D., Picard, H.R., Madden, T.K., Thruman, H.A., Kim, Y., Groutas, W.C., Chang, K.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI130092
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Author supporting evidence, Database references, Structure summary