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Crystal structure of the AMPA subunit GLUR2 bound to the allosteric modulator, trichlormethiazide

Analyse Crystal structure of the AMPA subunit GLUR2 bound to the allosteric modulator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ILT
Type: protein
Length: 774 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: GLU, TRU, ZN
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E, H	Glutamate receptor 2	protein	258	37% helix, 24% strand	P19491

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains B, E, H
TRU · 6-chloro-3-(dichloromethyl)-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide · ligand · 3 copies · chains B, E, H
ZN · Zinc ion · metal · 5 copies · chains B, H, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	611	0.73	0.80	89	TRU
2	931	0.70	0.75	73	empty
3	192	0.55	0.80	25	empty
4	93	0.47	0.81	20	empty
5	116	0.37	0.73	23	empty

Interfaces

3 interfaces between chains.

B–E · 1050 Å² buried · 11 hydrogen bonds · protein-protein
B–H · 230 Å² buried · 7 hydrogen bonds · protein-protein
E–H · 66 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3ILT · Crystal structure of the AMPA subunit GluR2 bound to the allosteric modulator… · the same entry in another collection · chain H against H, TM-score 1.00
P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P19491
Elsewhere: RCSB PDB 3ILT · PDBe 3ILT · UniProt P19491

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