› 6q01

X-ray diffraction
0.85Å resolution

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2

Released:
DOI: 10.2210/pdb6q01/pdb
PDB entry 6q01 coloured by chain, front view.
PDB entry 6q01 coloured by chain, side view.
PDB entry 6q01 coloured by chain, top view.
Source organisms:
Primary publication:
Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA, Cortés-Ledesma F, Williams RS
Nucleic Acids Res 48 6310-6325 (2020)
PMID: 32356875

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-131949 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: A, B
Molecule details ›
Chains: A, 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
Tyrosyl-DNA phosphodiesterase 2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 45 amino acids
Theoretical weight: 5.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O95551 (Residues: 25-66; Coverage: 12%)
Gene names: AD-022, EAP2, TDP2, TTRAP
Sequence domains: UBA-like domain

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand EDO 1 x EDO
Ligand K 3 x K
Ligand BEZ 1 x BEZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 53.793Å b: 65.461Å c: 67.677Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.101 0.1 0.114
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Human topoisomerases and their roles in genome stability and organization.
Pommier et al. (2022)
3 more

1 mention without citation

Exploring the protective mechanism of baicalin in treatment of atherosclerosis using endothelial cells deregulation model and network pharmacology.
Li et al. (2022)