7DK1 | pdb_00007dk1

Crystal structure of Zinc bound SARS-CoV-2 main protease

• PDB DOI: https://doi.org/10.2210/pdb7DK1/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-22 Released: 2021-06-30 
• Deposition Author(s): Sonkar, K.S., Panchariya, L., Kuila, S., Khan, W.A., Arockiasamy, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.209 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Zinc 2+ ion inhibits SARS-CoV-2 main protease and viral replication in vitro.

Panchariya, L., Khan, W.A., Kuila, S., Sonkar, K., Sahoo, S., Ghoshal, A., Kumar, A., Verma, D.K., Hasan, A., Khan, M.A., Jain, N., Mohapatra, A.K., Das, S., Thakur, J.K., Maiti, S., Nanda, R.K., Halder, R., Sunil, S., Arockiasamy, A.

(2021) Chem Commun (Camb) 57: 10083-10086

• PubMed: 34514483 
• DOI: https://doi.org/10.1039/d1cc03563k
• Primary Citation Related Structures: 
  7DK1


• PubMed Abstract: 
  

  Zinc deficiency is linked to poor prognosis in COVID-19 patients while clinical trials with zinc demonstrate better clinical outcomes. The molecular targets and mechanistic details of the anti-coronaviral activity of zinc remain obscure. We show that zinc not only inhibits the SARS-CoV-2 main protease (Mpro) with nanomolar affinity, but also viral replication. We present the first crystal structure of the Mpro-Zn ²⁺ complex at 1.9 Å and provide the structural basis of viral replication inhibition. We show that Zn ²⁺ coordinates with the catalytic dyad at the enzyme active site along with two previously unknown water molecules in a tetrahedral geometry to form a stable inhibited Mpro-Zn ²⁺ complex. Further, the natural ionophore quercetin increases the anti-viral potency of Zn ²⁺ . As the catalytic dyad is highly conserved across SARS-CoV, MERS-CoV and all variants of SARS-CoV-2, Zn ²⁺ mediated inhibition of Mpro may have wider implications.

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Organizational Affiliation: 
• Membrane Protein Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India. [e-mail].
Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
CSIR-Institute of Genomics and Integrative Biology, Near Jubilee Hall, Mall Road, Delhi-110007, India.
Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi-110067, India.
Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110 067, India.
CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
Ruhvenile Biomedical OPC PVT LTD, Plot No-8, OCF Pocket Institution, Sarita Vihar, New Delhi-110070, India.

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: 68.48 kDa 
• Atom Count: 5,045 
• Modeled Residue Count: 605 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	L [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
DMS	E [auth A], H [auth B], J [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
GLY	F [auth A], K [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.209 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37dk1

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.62	α = 90
b = 102.2	β = 90
c = 102.35	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
Coot	model building
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Sonkar, K.S., Panchariya, L., Kuila, S., Khan, W.A., Arockiasamy, A.

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2022-03-30
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description