Research workbench

Crystal structure of IGLUR2 ligand binding domain with symmetric sulfonamide containing potentiator

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

PDB: 3RNN
Type: protein
Length: 776 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P42262
Ligands: GLU, RNN, ZN
Pockets: 5 · best druggability 0.83

Structure

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

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

Ligands and binding sites

GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
RNN · N,N'-(benzene-1,4-diyldiethane-2,1-diyl)dipropane-2-sulfonamide · ligand · 2 copies · chains A, C, B
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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1036	0.83	0.84	133	RNN
2	282	0.58	0.78	29	empty
3	85	0.43	0.79	23	empty
4	84	0.40	0.78	20	empty
5	83	0.37	0.76	23	empty

Interfaces

3 interfaces between chains.

A–C · 921 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 285 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 74 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3RNN · Crystal Structure of iGluR2 Ligand Binding Domain with Symmetric Sulfonamide 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 3RNN · PDBe 3RNN · UniProt P42262

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