5r8t

X-ray diffraction
1.27Å resolution

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease screened against DSI poised (Enamine), Fraglites and Peplites (Newcastle university), Mini Frags (Astex), York 3D (York university), electrophile cysteine covalent (Weizman institute) fragment libraries

Released:
Entry authors: Fearon D, Owen CD, Douangamath A, Lukacik P, Powell AJ, Strain-Damerell CM, Resnick E, Krojer T, Gehrtz P, Wild C, Aimon A, Brandao-Neto J, Carbery A, Dunnett L, Skyner R, Snee M, London N, Walsh MA, von Delft F

Function and Biology Details

Reactions catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase nsp5 Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.83 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 112.207Å b: 52.596Å c: 44.631Å
α: 90° β: 102.99° γ: 90°
R-values:
R R work R free
0.185 0.184 0.208
Expression system: Escherichia coli