› 5yj8

X-ray diffraction
1.76Å resolution

Identification of a small molecule inhibitor for the Tudor domain of TDRD3

Released:
DOI: 10.2210/pdb5yj8/pdb
PDB entry 5yj8 coloured by chain, front view.
PDB entry 5yj8 coloured by chain, side view.
PDB entry 5yj8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.
Liu J, Zhang S, Liu M, Liu Y, Nshogoza G, Gao J, Ma R, Yang Y, Wu J, Zhang J, Li F, Ruan K
FEBS J 285 2091-2103 (2018)
PMID: 29645362

Function and Biology Details

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-574440 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tudor domain-containing protein 3 Chain: A
Molecule details ›
Chain: A
Length: 60 amino acids
Theoretical weight: 7.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q9H7E2 (Residues: 555-608; Coverage: 8%)
Gene name: TDRD3
Sequence domains: Tudor domain
Structure domains: SH3 type barrels.

Ligands and Environments

2 bound ligands:
Ligand 8W9 1 x 8W9
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P3221
Unit cell:
a: 50.974Å b: 50.974Å c: 42.087Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.187 0.226
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

1 review citation

Targeting epigenetic protein-protein interactions with small-molecule inhibitors.
Linhares et al. (2020)
6 other articles

1 mention without citation

Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.
Liu et al. (2018)