› 7c8u

X-ray diffraction
2.35Å resolution

The crystal structure of COVID-19 main protease in complex with GC376

Released:
DOI: 10.2210/pdb7c8u/pdb
PDB entry 7c8u coloured by chain, front view.
PDB entry 7c8u coloured by chain, side view.
PDB entry 7c8u coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Entry authors: Luan X, Shang W, Wang Y, Yin W, Jiang Y, Feng S, Wang Y, Liu M, Zhou R, Zhang Z, Wang F, Cheng W, Gao M, Wang H, Wu W, Tian R, Tian Z, Jin Y, Jiang HW, Zhang L, Xu HE, Zhang S

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
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145080 (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
Sequence domains: Coronavirus endopeptidase C30

Ligands and Environments

1 bound ligand:
Ligand K36 1 x K36
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2
Unit cell:
a: 114.303Å b: 53.874Å c: 45.233Å
α: 90° β: 101.576° γ: 90°
R-values:
R R work R free
0.215 0.212 0.273
Expression system: Escherichia coli

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