Crystal structure of the GLUA2O lbd in complex with glutamate and tak- 653

Structure

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

Ligands and binding sites

• GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
• 0YK · 7-(4-cyclohexyloxyphenyl)-9-methyl-4$l^{6}-thia-1$l^{4},5,8-triazabicyclo[4.4.0]deca-1(10),6,8-triene 4,4-dioxide · ligand · 3 copies · chains A, B, C, D, E, F
• ZN · Zinc ion · metal · 10 copies · chains B, A, C, D, E, F
• ACT · Acetate ion · additive · 4 copies · chains C, D, F
• GOL · Glycerol · additive · 2 copies · chains C, D

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• A–B · 996 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 980 Ų buried · 11 hydrogen bonds · protein-protein
• E–F · 975 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 331 Ų buried · 10 hydrogen bonds · protein-protein
• D–E · 326 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 7F3O · Crystal structure of the GluA2o LBD in complex with glutamate and TAK-653 · the same entry in another collection · chain F against F, TM-score 1.00
• P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · a predicted model of the same protein · chain E 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 7F3O · PDBe 7F3O · UniProt P42262