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Crystal structure of the AMPA subunit GLUR2 bound to the allosteric modulator, idra-21

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: 3IL1
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, B5D, ZN
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E, H	Glutamate receptor 2	protein	258	38% helix, 21% strand	P19491

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains B, E, H
B5D · (3S)-7-chloro-3-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 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

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1162	0.82	0.83	137	B5D
2	296	0.61	0.79	33	empty
3	233	0.50	0.75	41	empty
4	92	0.39	0.76	22	empty
5	79	0.35	0.75	23	empty

Interfaces

3 interfaces between chains.

B–E · 814 Å² buried · 8 hydrogen bonds · protein-protein
B–H · 259 Å² buried · 5 hydrogen bonds · protein-protein
E–H · 63 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3IL1 · Crystal structure of the AMPA subunit GluR2 bound to the allosteric modulator, IDRA-21 · the same entry in another collection · chain E against E, 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 0.98

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 P19491
Elsewhere: RCSB PDB 3IL1 · PDBe 3IL1 · UniProt P19491

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