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Structure of the ligand-binding core of the ionotropic glutamate receptor-like GLURDELTA2 in the apo form

Analyse Structure of the ligand-binding core of the ionotropic glutamate receptor-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V3T
Type: protein
Length: 498 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor delta-2 subunit synonym GLURDELTA2, glur delta-2
UniProt: Q63226
Ligands: CA
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor delta-2 subunit synonym GLURDELTA2, glur delta-2	protein	244	36% helix, 24% strand	Q63226
B	Glutamate receptor delta-2 subunit synonym GLURDELTA2, glur delta-2	protein	254	36% helix, 24% strand	Q63226

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

5 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	806	0.71	0.77	85	empty
2	228	0.59	0.80	38	empty
3	329	0.59	0.77	39	empty
4	57	0.29	0.75	16	empty
5	55	0.27	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 1196 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified, 1 disulfide (engineered, disulfide).

Compared structures

2V3T · Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2… · the same entry in another collection · chain A against A, TM-score 1.00
Q63226 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, delta-2 (Q63226) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q63226
Elsewhere: RCSB PDB 2V3T · PDBe 2V3T · UniProt Q63226

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