Crystal structure of T-cell lymphoma invasion and metastasis-1 PDZ domain quadruple mutant (qm) in complex with neurexin-1 peptide

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 42% strand (DSSP).

Ligands and binding sites

• ANS · 5-(dimethylamino)-1-naphthalenesulfonic acid(dansyl acid) · ligand · chains A, B
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 563 Ų buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 4NXR · Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple… · 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 0.85
• P58401 · AlphaFold monomer V2.0 prediction for neurexin-2-beta (P58401) · a predicted model of the same protein · chain B against A, TM-score 0.58

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 P58401
• Elsewhere: RCSB PDB 4NXR · PDBe 4NXR · UniProt Q13009 · UniProt P58401