Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).

Ligands and binding sites

• PWT · 2-[[2-(5-oxidanylidenepentanoyl) hydrazinyl]methyl]benzoic acid · ligand · 2 copies · chains A, B

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

Interfaces

1 interface between chains.

• A–B · 1028 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6YX1 · Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y566 · AlphaFold monomer V2.0 prediction for SH3 and multiple ankyrin repeat domains protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q9Y566
• Elsewhere: RCSB PDB 6YX1 · PDBe 6YX1 · UniProt Q9Y566