Crystal structure of the third PDZ domain of sap-102 in complex with a fluorogenic peptide-based ligand

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 36% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains A, C, D, B
• ACT · Acetate ion · additive · chains A, B, C, D

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

Interfaces

6 interfaces between chains.

• B–C · 562 Ų buried · 14 hydrogen bonds · protein-protein
• A–D · 533 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 498 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 133 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 126 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

• 3JXT · Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic… · the same entry in another collection · chain D against D, TM-score 1.00
• Q62936 · AlphaFold monomer V2.0 prediction for disks large homolog 3 (Q62936) · a predicted model of the same protein · chain B against A, TM-score 0.95
• O88602 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-2 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.66

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 Q62936
• Every structure of UniProt O88602
• Elsewhere: RCSB PDB 3JXT · PDBe 3JXT · UniProt Q62936 · UniProt O88602