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)

Macromolecule Content

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2450 
• Modelled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

7K6E

SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.63 A Resolution (Direct Vitrification)

• PDB DOI: 10.2210/pdb7K6E/pdb

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


• Deposited: 2020-09-19 Released: 2020-09-30 
• Deposition Author(s): Kreitler, D.F., Andi, B., Kumaran, D., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Brookhaven National Laboratory (BNL), National Virtual Biotechnology Laboratory (NVBL

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.245 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.63 A Resolution (Direct Vitrification)

Kreitler, D.F., Andi, B., Kumaran, D., Soares, A.S., Jakoncic, J., Fuchs, M., Keereetaweep, J., Shanklin, J., McSweeney, S.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
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
SV6 (Subject of Investigation/LOI)	C [auth A]	(1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide C36 H55 N7 O6 FTZGWEAUHOMNIG-FJRGXGLZSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002448 (SV6)	C [auth A]	TELAPREVIR, bound form	Peptide-like / Antiviral		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.245 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 54.71	β = 101.231
c = 48.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AutoProcess	data reduction
XDS	data reduction
XSCALE	data scaling
Aimless	data processing
pointless	data processing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-09-19 
• Released Date: 2020-09-30 
Deposition Author(s): Kreitler, D.F., Andi, B., Kumaran, D., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	KP1605010
Brookhaven National Laboratory (BNL)	United States	LDRD 20-042
National Virtual Biotechnology Laboratory (NVBL	United States	Coronavirus CARES Act

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2021-01-27
  Changes: Structure summary