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6woj

X-ray diffraction
2.2Å resolution

Structure of the SARS-CoV-2 macrodomain (NSP3) in complex with ADP-ribose

Released:
Model geometry
Fit model/data

Function and Biology Details

Reactions catalysed:
a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleosidein mRNA + S-adenosyl-L-homocysteine.
a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA +S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+).
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate.
a 5'-end diphospho-ribonucleoside in mRNA + GTP + H(+) = a 5'-end(5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate.
Thiol-dependent hydrolysis of ester, thioester, amide, peptide andisopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residueprotein attached to proteins as an intracellular targeting signal).
TSAVLQ-|-SGFRK-NH2 and SGVTFQ-|-GKFKK the two peptides corresponding tothe two self-cleavage sites of the SARS 3C-like proteinase are the twomost reactive peptide substrates. The enzyme exhibits a strong preferencefor substrates containing Gln at P1 position and Leu at P2 position.
ATP + H2O = ADP + phosphate + H(+).
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 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 176 amino acids
Theoretical weight: 18.99 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 1023-1197; Coverage: 3%)
Gene names: 1a-1b, rep
Sequence domains: Macro domain

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 59.715Å b: 83.165Å c: 84.237Å
α: 90° β: 94.37° γ: 90°
R-values:
R R work R free
0.202 0.199 0.252
Expression system: Escherichia coli BL21(DE3)