MolNFT v1 · #109488 · protein

Crystal structure of GLUR2 ligand-binding core

4X48 · Glutamate receptor 2: “Crystal structure of GLUR2 ligand-binding core”. X-ray diffraction, 3 ligands (GLU, XPF, ZN), 5 pockets (best druggability 0.83). MolNFT v1 #109488 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X48
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, XPF, ZN
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 37% 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	36% helix, 21% strand	P19491

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
XPF · N-{(3S,4S)-4-[4-(5-cyanothiophen-2-yl)phenoxy]tetrahydrofuran-3-yl}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

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	1110	0.83	0.84	134	XPF
2	278	0.60	0.79	33	empty
3	192	0.52	0.78	36	empty
4	94	0.39	0.76	26	empty
5	61	0.34	0.77	20	empty

Interfaces

3 interfaces between chains.

A–C · 917 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 331 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 75 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4X48 · Crystal structure of GluR2 ligand-binding core · 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 4X48 · PDBe 4X48 · UniProt P19491

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.