7h14

X-ray diffraction
1.15Å resolution

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0013383-001

Released:
Entry authors: Aschenbrenner JC, Fearon D, Tomlinson CWE, Marples PG, Fairhead M, Balcomb BH, Chandran AV, Godoy AS, Koekemoer L, Lithgo RM, Ni X, Thompson W, Wang S, Wild C, Williams EP, Winokan M, Walsh MA, von Delft F

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:
  • not assigned
Biological process:
  • not assigned
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: 170 amino acids
Theoretical weight: 18.28 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 1024-1192; Coverage: 2%)
Gene names: 1a-1b, rep
Sequence domains: Macro domain

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 38.346Å b: 33.153Å c: 64.175Å
α: 90° β: 101.33° γ: 90°
R-values:
R R work R free
0.16 0.158 0.189
Expression system: Escherichia coli