› 5zq4

X-ray diffraction
2.22Å resolution

PDE-Ubi-ADPr

Released:
DOI: 10.2210/pdb5zq4/pdb
PDB entry 5zq4 coloured by chain, front view.
PDB entry 5zq4 coloured by chain, side view.
PDB entry 5zq4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.
Wang Y, Shi M, Feng H, Zhu Y, Liu S, Gao A, Gao P
Cell 173 1231-1243.e16 (2018)
PMID: 29731171

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143382 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SidE Chains: A, B
Molecule details ›
Chains: A, B
Length: 377 amino acids
Theoretical weight: 43.58 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6BBR6 (Residues: 240-608; Coverage: 24%)
Gene name: laiD
Sequence domains: SidE phosphodiesterase (PDE) domain
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 78 amino acids
Theoretical weight: 8.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 95.417Å b: 55.384Å c: 98.435Å
α: 90° β: 110.22° γ: 90°
R-values:
R R work R free
0.183 0.181 0.226
Expression system: Escherichia coli

Quick links

Citations

15 review citations

The role of ubiquitination in tumorigenesis and targeted drug discovery.
Deng et al. (2020)
14 more

1 mention without citation

Uncovering the Structural Basis of a New Twist in Protein Ubiquitination.
Puvar et al. (2019)