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.

Macromolecule Content

• Total Structure Weight: 34.75 kDa 
• Atom Count: 2970 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

7K3T

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) at 1.2 A Resolution and a Possible Capture of Zinc Binding Intermediate

• PDB DOI: 10.2210/pdb7K3T/pdb

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


• Deposited: 2020-09-13 Released: 2020-09-23 
• Deposition Author(s): Andi, B., Kumaran, D., Kreitler, D.F., 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: 1.20 Å
• R-Value Free: 0.167 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 

Literature

Drug-Like Compounds as Efficient Covalent Binders of the SARS-CoV-2 Main Protease 3CLPro: Hepatitis C Virus NS3/4A Inhibitors and Others

Andi, B., Kumaran, D., Kreitler, D.F., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., 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
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.167 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.784	α = 90
b = 52.931	β = 100.07
c = 111.273	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-09-13 
• Released Date: 2020-09-23 
Deposition Author(s): Andi, B., Kumaran, D., Kreitler, D.F., 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: 2020-09-23
  Type: Initial release
  
• Version 2.0: 2022-03-16
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary