SMTL ID : 8s6a.1

X-ray structure of Dishevelled 3 PDZ domain in a complex with a class III peptide ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

1 x SER- GLU- PHE- PHE- VAL- ASP- VAL- MET: C8 peptide(Non-covalent)

SER-GLU-PHE-PHE-VAL-ASP-VAL-MET.1: 27 residues within 4Å: Chain A: F.19, L.20, G.21, I.22, S.23, I.24, V.25, S.40, M.42, V.76, L.79, R.80, V.83 Chain B: F.19, L.20, G.21, I.22, I.24, V.25, G.26, Q.27, M.42, N.72, D.73, V.76, R.80, V.83 36 PLIP interactions: 15 interactions with chain A, 21 interactions with chain B Hydrophobic interactions: A:V.25, A:V.76, A:L.79, A:L.79, B:I.22, B:I.24, B:V.25, B:D.73, B:V.76 Hydrogen bonds: A:L.20, A:G.21, A:I.22, A:I.22, A:S.23, A:I.24, A:I.24, A:S.40, A:S.40, A:R.80, B:L.20, B:G.21, B:I.22, B:I.22, B:I.24, B:G.26, B:G.26, B:Q.27, B:Q.27, B:R.80 Water bridges: A:I.22, B:I.24, B:G.26, B:N.72, B:D.73, B:D.73 Salt bridges: B:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, J. et al., A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain. Structure (2025)

Release Date

2025-03-12

Peptides

Segment polarity protein dishevelled homolog DVL-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Segment polarity protein dishevelled homolog DVL-3