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Structure of the ligand-binding core of GLUR2 in complex with the agonist (R)-tdpa at 1.95 a resolution

Analyse Structure of the ligand-binding core of GLUR2 in complex with the agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BFU
Type: protein
Length: 1,044 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: R2P
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor 2	protein	262	37% helix, 21% strand	P19491
B, D	Glutamate receptor 2	protein	260	37% helix, 20% strand	P19491
C	Glutamate receptor 2	protein	262	37% helix, 21% strand	P19491

Ligands and binding sites

R2P · (2R)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	639	0.76	0.82	68	empty
2	55	0.71	0.98	19	R2P
3	52	0.71	0.99	18	R2P
4	52	0.69	0.97	18	R2P
5	50	0.68	0.97	18	R2P

Interfaces

4 interfaces between chains.

A–D · 517 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 382 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 376 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 198 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3BFU · Structure of the ligand-binding core of GluR2 in complex with the agonist (R)-TDPA at… · the same entry in another collection · chain A against A, 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 3BFU · PDBe 3BFU · UniProt P19491

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