8QDC image
Deposition Date 2023-08-28
Release Date 2024-07-03
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8QDC
Keywords:
VIRAL PROTEIN
Title:
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalent inhibitor GUE-3642 (compound 1 in publication)
Biological Source:
Source Organism:
Severe acute respiratory syndrome coronavirus (Taxon ID: 2901879)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.77 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
8QDC validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:3C-like proteinase nsp5
Gene (Uniprot):rep
Chain IDs:A, B
Chain Length:306
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus
UniProt ID:P0DTD1 Pfam ID:PF05409 EC:2.7.7.48
Ligand Molecules
CL
DMS
XV9
Primary Citation
Development of an active-site titrant for SARS-CoV-2 main protease as an indispensable tool for evaluating enzyme kinetics.
Acta Pharm Sin B 14 2349 2357 (2024)
PMID: 38799620 DOI: 10.1016/j.apsb.2024.03.001

Abstact

A titrant for the SARS-CoV-2 main protease (Mpro) was developed that enables, for the first time, the exact determination of the concentration of the enzymatically active Mpro by active-site titration. The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme-titrant complex. Four fluorogenic substrates of Mpro, including a prototypical, internally quenched Dabcyl-EDANS peptide, were compared in terms of solubility under typical assay conditions. By exploiting the new titrant, key kinetic parameters for the Mpro-catalyzed cleavage of these substrates were determined.

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Primary Citation of related structures
8QDC