› 5bz0

X-ray diffraction
2.1Å resolution

Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin

Released:
DOI: 10.2210/pdb5bz0/pdb
PDB entry 5bz0 coloured by chain, front view.
PDB entry 5bz0 coloured by chain, side view.
PDB entry 5bz0 coloured by chain, top view.
Source organisms:
Entry authors: Kong LY, Yan LM, Zhang Y, Rao ZH

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143135 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Papain-like protease Chain: A
Molecule details ›
Chain: A
Length: 313 amino acids
Theoretical weight: 34.98 KDa
Source organism: Avian infectious bronchitis virus (strain Beaudette)
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6Y1 (Residues: 1174-1483; Coverage: 5%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus papain-like peptidase
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P62992 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 63.058Å b: 74.812Å c: 95.502Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.228
Expression system: Escherichia coli

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