› 2vri

X-ray diffraction
1.9Å resolution

Structure of the NSP3 X-domain of human coronavirus NL63

Released:
DOI: 10.2210/pdb2vri/pdb
PDB entry 2vri coloured by chain, front view.
PDB entry 2vri coloured by chain, side view.
PDB entry 2vri coloured by chain, top view.
Source organism: Human coronavirus NL63
Entry authors: Piotrowski Y, Mesters JR, Moll R, Hilgenfeld R

Function and Biology Details

Reaction catalysed: 
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).
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143067 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Non-structural protein 3 Chain: A
Molecule details ›
Chain: A
Length: 174 amino acids
Theoretical weight: 18.87 KDa
Source organism: Human coronavirus NL63
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C6U6 (Residues: 1254-1421; Coverage: 4%)
Gene name: 1a
Sequence domains: Macro domain
Structure domains: Leucine Aminopeptidase, subunit E, domain 1

Ligands and Environments

1 bound ligand:
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P212121
Unit cell:
a: 53.97Å b: 54.77Å c: 57.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.185 0.243
Expression system: Escherichia coli BL21(DE3)

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