Crystal structure of IGLUR2 ligand binding domain and symmetrical carboxyl containing potentiator

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).

Ligands and binding sites

• GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
• RN8 · 3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid) · ligand · 2 copies · chains A, C, B
• ZN · Zinc ion · metal · 5 copies · chains A, B, C
• SO4 · Sulfate ion · ion · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains B, C

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 906 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 307 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 3RN8 · Crystal Structure of iGluR2 Ligand Binding Domain and Symmetrical Carboxyl Containing… · the same entry in another collection · chain A against A, TM-score 1.00
• P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P42262
• Elsewhere: RCSB PDB 3RN8 · PDBe 3RN8 · UniProt P42262