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SARS-CoV-2 Mpro mutant (H41A) in complex with nsp6|7 peptidyl substrate

X-ray diffraction
1.8Å resolution
PDB entry 7dvx coloured by chain, front view.
PDB entry 7dvx coloured by chain, side view.
PDB entry 7dvx coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SARS-CoV-2 primase complex
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Multimeric state: hetero tetramer
Accessible surface area: 25719.15 Å2
Buried surface area: 5944.73 Å2
Dissociation area: 1,427.41 Å2
Dissociation energy (ΔGdiss): 12.46 kcal/mol
Dissociation entropy (TΔSdiss): 13.95 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-145081
Complex Portal ID: CPX-5690

Macromolecules

3C-like proteinase nsp5
Chain: A
Length: 306 amino acids
Theoretical weight: 33.76 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep
Pfam: Coronavirus endopeptidase C30
InterPro:
3C-like proteinase nsp5 in PDB entry 7dvx, assembly 1, front view.
3C-like proteinase nsp5 in PDB entry 7dvx, assembly 1, side view.
3C-like proteinase nsp5 in PDB entry 7dvx, assembly 1, top view.
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Non-structural protein 7
Chain: C
Length: 20 amino acids
Theoretical weight: 2.16 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Not provided
UniProt:
  • Canonical: P0DTD1 (Residues: 3850-3869; Coverage: 0%)
Gene names: 1a-1b, rep
Non-structural protein 7 in PDB entry 7dvx, assembly 1, front view.
Non-structural protein 7 in PDB entry 7dvx, assembly 1, side view.
Non-structural protein 7 in PDB entry 7dvx, assembly 1, top view.
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