› 4rg2

X-ray diffraction
1.5Å resolution

Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand

Released:
DOI: 10.2210/pdb4rg2/pdb
PDB entry 4rg2 coloured by chain, front view.
PDB entry 4rg2 coloured by chain, side view.
PDB entry 4rg2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1.
Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV
ACS Chem Biol 10 1072-81 (2015)
PMID: 25590533

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171427 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
TP53-binding protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 125 amino acids
Theoretical weight: 14.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12888 (Residues: 1483-1606; Coverage: 6%)
Gene name: TP53BP1
Sequence domains: Tumour suppressor p53-binding protein-1 Tudor
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 3OO 1 x 3OO
Ligand EDO 3 x EDO
Ligand UNX 12 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 73.548Å b: 100.458Å c: 83.348Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.197 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

The Chemical Biology of Reversible Lysine Post-translational Modifications.
Wang et al. (2020)
9 more

4 mentions without citation

Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy.
McPherson et al. (2021)
3 more