MolNFT v1 · #99292 · protein

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

4LZ5 · Glutamate receptor 2: “Crystal structures of GLUR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators”. X-ray diffraction, 3 ligands (GLU, 1YV, ZN), 6 pockets (best druggability 0.83). MolNFT v1…

PDB: 4LZ5
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, 1YV, ZN
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

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

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
1YV · N-[(2R)-2-(4'-cyanobiphenyl-4-yl)propyl]propane-2-sulfonamide · 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

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	1118	0.83	0.84	151	1YV
2	292	0.58	0.78	33	empty
3	171	0.45	0.75	27	empty
4	106	0.42	0.77	27	empty
5	58	0.33	0.77	14	empty

Interfaces

3 interfaces between chains.

A–C · 884 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 273 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 75 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4LZ5 · Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive… · the same entry in another collection · chain C against C, 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 4LZ5 · PDBe 4LZ5 · UniProt P19491

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