SMTL ID : 8jtn.1

Tudor domain of TDRD3 in complex with a small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x F5W: 2-propyl-2-azoniatricyclo[7.3.0.0^{3,7}]dodeca-1(9),2,7-trien-8-amine(Non-covalent)

F5W.1: 6 residues within 4Å: Chain A: Y.14, D.17, Y.21, F.39, Y.42, N.44 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.14, A:Y.14, A:Y.21, A:Y.21, A:F.39, A:Y.42, A:Y.42, A:Y.42 Hydrogen bonds: A:N.44 pi-Stacking: A:Y.42 F5W.2: 3 residues within 4Å: Chain A: W.15, E.47, L.49 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.15, A:L.49 Hydrogen bonds: A:E.47, A:E.47 F5W.3: 5 residues within 4Å: Chain A: L.13, N.18, F.20, S.51, N.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.20 Hydrogen bonds: A:N.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Crystal structure of Tudor domain of TDRD3 in complex with a small molecule antagonist. Biochim Biophys Acta Gene Regul Mech (2023)

Release Date

2023-08-09

Peptides

Tudor domain-containing protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tudor domain-containing protein 3