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Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl phenyl sulfane inhibitor (cyano warhead)

X-ray diffraction
1.5Å resolution
PDB entry 8f46 coloured by chain, front view.
PDB entry 8f46 coloured by chain, side view.
PDB entry 8f46 coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Assembly composition:
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SARS-CoV-2 NSP9 complex
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Multimeric state: homo dimer
Accessible surface area: 25009.94 Å2
Buried surface area: 2539.84 Å2
Dissociation area: 1,038.26 Å2
Dissociation energy (ΔGdiss): 6.36 kcal/mol
Dissociation entropy (TΔSdiss): 13.73 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-145080
Complex Portal ID: CPX-5687

Macromolecules

3C-like proteinase nsp5
Chains: A, B
Length: 309 amino acids
Theoretical weight: 34.07 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3568; Coverage: 4%)
Gene names: 1a-1b, rep
Pfam: Coronavirus endopeptidase C30
InterPro:
3C-like proteinase nsp5 in PDB entry 8f46, assembly 1, front view.
3C-like proteinase nsp5 in PDB entry 8f46, assembly 1, side view.
3C-like proteinase nsp5 in PDB entry 8f46, assembly 1, top view.
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