9O6Q

Crystal Structure of SARS-CoV-2 Mpro L115A in complex with Pfizer Intravenous Inhibitor PF-00835231

Summary for 9O6Q

• Entry DOI: 10.2210/pdb9o6q/pdb
• Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide (3 entities in total)
• Functional Keywords: sars2, sars-cov-2, mpro, s10a, covid19, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 68516.03

Authors

Zvornicanin, S.N.,Shaqra, A.M.,Schiffer, C.A. (deposition date: 2025-04-14, release date: 2025-12-10, Last modification date: 2026-01-28)

Primary citation

Zvornicanin, S.N.,Shaqra, A.M.,Flynn, J.,Intravaia, L.E.,Martinez, H.C.,Jia, W.,Gupta, D.K.,Moquin, S.,Dovala, D.,Bolon, D.N.,Kelch, B.A.,Schiffer, C.A.,Yilmaz, N.K.
Cooperativity and communication between the active sites of the dimeric SARS-CoV-2 main protease.
Sci Adv, 12:eaeb0769-eaeb0769, 2026

PubMed Abstract: The coronaviral main protease (M) has been the subject of various biochemical and structural studies and a drug target against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. SARS-CoV-2 M is active as a dimer, but despite apparent cooperativity in catalytic activity, how the two distal active sites communicate and modulate binding and/or catalysis is unclear. Here, we have investigated the interplay between cooperativity, dimerization, and substrate cleavage in SARS-CoV-2 M through a combination of enzymatic assays, crystal structures, and protein characterization. To disentangle the contribution of each active site to the observed enzymatic activity, we developed a cleavage assay involving heterodimers of active and inactive (catalytic residue mutated or inhibitor-bound) monomers. Notably, we found that heterodimerization increased cleavage efficiency per active monomer. In addition, we mapped a network of critical residues bridging the two active sites and probed this network through engineered mutations. By dissecting the cooperativity and communication between the active sites, we provide insights into the M reaction cycle and functional significance of its dimeric architecture.

PubMed: 41544157
DOI: 10.1126/sciadv.aeb0769

Experimental method

X-RAY DIFFRACTION (2.21 Å)