7BFB | pdb_00007bfb

Crystal structure of ebselen covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.

• PDB DOI: https://doi.org/10.2210/pdb7BFB/pdb

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


• Deposited: 2021-01-02 Released: 2021-03-03 
• Deposition Author(s): Costanzi, E., Demitri, N., Giabbai, B., Storici, P.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ebselen covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.

Costanzi, E., Demitri, N., Giabbai, B., Storici, P.

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: 69.51 kDa 
• Atom Count: 4,905 
• Modeled Residue Count: 606 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Main Protease	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JT (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], L [auth B], O [auth B]	N-phenyl-2-selanylbenzamide C13 H11 N O Se PVPUYGNPKBMXGO-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	J [auth A], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.739	α = 90
b = 100.455	β = 90
c = 104.597	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Costanzi, E., Demitri, N., Giabbai, B., Storici, P.

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Funding Organization	Location	Grant Number
European Commission	European Union	101003551

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2023-04-12
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary