› 5nh0

X-ray diffraction
2.35Å resolution

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl)

Released:
DOI: 10.2210/pdb5nh0/pdb
PDB entry 5nh0 coloured by chain, front view.
PDB entry 5nh0 coloured by chain, side view.
PDB entry 5nh0 coloured by chain, top view.
Source organism: Human coronavirus NL63
Entry authors: Zhang L, Hilgenfeld R

Function and Biology Details

Reactions catalysed: 
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).
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143100 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 300 amino acids
Theoretical weight: 32.41 KDa
Source organism: Human coronavirus NL63
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6X5 (Residues: 2940-3239; Coverage: 5%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus endopeptidase C30
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 8X8 3 x 8X8
Ligand DMS 3 x DMS
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: C2221
Unit cell:
a: 133.65Å b: 211.29Å c: 118.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.232
Expression system: Escherichia coli

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