Crystal structure of T-cell lymphoma invasion and metastasis-1 PDZ in complex with SYNDECAN1 peptide

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).

Ligands and binding sites

• ANS · 5-(dimethylamino)-1-naphthalenesulfonic acid(dansyl acid) · ligand · 2 copies · chains B, C, A, D
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 3 copies · chains A, B

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

Interfaces

4 interfaces between chains.

• B–C · 567 Ų buried · 16 hydrogen bonds · protein-protein
• A–B · 504 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 476 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 232 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4GVD · Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q13009 · AlphaFold monomer V2.0 prediction for T-lymphoma invasion and metastasis-inducing protein… · a predicted model of the same protein · chain A against A, TM-score 0.92
• P18827 · AlphaFold monomer V2.0 prediction for syndecan-1 (P18827) · a predicted model of the same protein · chain C against A, TM-score 0.35

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 Q13009
• Every structure of UniProt P18827
• Elsewhere: RCSB PDB 4GVD · PDBe 4GVD · UniProt Q13009 · UniProt P18827