› 2ynb

X-ray diffraction
1.96Å resolution

Crystal structure of the main protease of coronavirus HKU4 in complex with a Michael acceptor SG85

Released:
DOI: 10.2210/pdb2ynb/pdb
PDB entry 2ynb coloured by chain, front view.
PDB entry 2ynb coloured by chain, side view.
PDB entry 2ynb coloured by chain, top view.
Source organism: Tylonycteris bat coronavirus HKU4
Entry authors: Ma Q, Xiao Y, Hilgenfeld R

Function and Biology Details

Reactions catalysed: 
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.
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-143062 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase nsp5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 306 amino acids
Theoretical weight: 33.22 KDa
Source organism: Tylonycteris bat coronavirus HKU4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C6T4 (Residues: 3292-3597; Coverage: 7%)
Gene name: 1a
Sequence domains: Coronavirus endopeptidase C30
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NI 2 x NI
Ligand G85 1 x G85
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P3121
Unit cell:
a: 79.35Å b: 79.35Å c: 178.67Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.171 0.198
Expression system: Escherichia coli BL21(DE3)

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