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Crystal structure of IGLUR2 ligand binding domain and symmetrical carboxyl containing potentiator

Analyse Crystal structure of IGLUR2 ligand binding domain and symmetrical carboxyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RN8
Type: protein
Length: 775 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P42262
Ligands: GLU, RN8, ZN, SO4
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 2	protein	258	38% helix, 21% strand	P42262
B	Glutamate receptor 2	protein	259	37% helix, 21% strand	P42262

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
RN8 · 3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid) · ligand · 2 copies · chains A, C, B
ZN · Zinc ion · metal · 5 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A, B
ACT · Acetate ion · additive · 2 copies · chains B, C

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

Pockets

8 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	817	0.82	0.84	117	RN8, ACT
2	274	0.63	0.81	29	empty
3	254	0.56	0.78	26	empty
4	116	0.42	0.76	32	empty
5	112	0.41	0.77	21	empty

Interfaces

3 interfaces between chains.

A–C · 906 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 307 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 84 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3RN8 · Crystal Structure of iGluR2 Ligand Binding Domain and Symmetrical Carboxyl Containing… · the same entry in another collection · chain A against A, TM-score 1.00
P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · 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 P42262
Elsewhere: RCSB PDB 3RN8 · PDBe 3RN8 · UniProt P42262

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