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Crystal structures of GLUR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators

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

PDB: 4LZ7
Type: protein
Length: 772 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: GLU, 1YW, ZN
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor 2	protein	258	38% helix, 23% strand	P19491
B, C	Glutamate receptor 2	protein	257	37% helix, 21% strand	P19491

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
1YW · N-({(5S)-3-[3-fluoro-4-(pyrrolidin-1-yl)phenyl]-4,5-dihydro-1,2-oxazol-5-yl}methyl)acetamide · ligand · 2 copies · chains B, A, C
ZN · Zinc ion · metal · 5 copies · chains A, B, C

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

Pockets

7 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	1088	0.83	0.84	139	1YW
2	258	0.58	0.79	31	empty
3	94	0.44	0.80	22	empty
4	92	0.43	0.79	24	empty
5	97	0.40	0.77	26	empty

Interfaces

3 interfaces between chains.

A–C · 883 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 299 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 72 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4LZ7 · Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive… · 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 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 P19491
Elsewhere: RCSB PDB 4LZ7 · PDBe 4LZ7 · UniProt P19491

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