7sgv

X-ray diffraction
2Å resolution

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor

Released:
Entry authors: Osipiuk J, Tesar C, Endres M, Lisnyak V, Maki S, Taylor C, Zhang Y, Zhou Z, Azizi SA, Jones K, Kathayat R, Snyder SA, Dickinson BC, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
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]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
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).
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.
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-145022 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Papain-like protease nsp3 Chain: A
Molecule details ›
Chain: A
Length: 318 amino acids
Theoretical weight: 35.93 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 1564-1878; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus papain-like peptidase

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3221
Unit cell:
a: 82.982Å b: 82.982Å c: 134.021Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.181 0.207
Expression system: Escherichia coli BL21(DE3)