The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ- binding motif of RSK1

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 10% strand (DSSP).

Ligands and binding sites

• CA · Calcium ion · metal · 4 copies · chains A
• GOL · Glycerol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 421 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

• 7P74 · The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1 · the same entry in another collection · chain A against A, TM-score 1.00
• Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain B against A, TM-score 0.92
• P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain A against A, TM-score 0.77
• P57105 · AlphaFold monomer V2.0 prediction for synaptojanin-2-binding protein (P57105) · a predicted model of the same protein · chain A against A, TM-score 0.25

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P57105
• Every structure of UniProt P07355
• Every structure of UniProt Q15418
• Elsewhere: RCSB PDB 7P74 · PDBe 7P74 · UniProt P57105 · UniProt P07355 · UniProt Q15418