Research workbench

AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive inhibitor perampanel

Analyse AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L1F
Type: protein
Length: 3,100 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: 6ZP, NAG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Glutamate receptor 2	protein	777	40% helix, 18% strand	P19491
B, C	Glutamate receptor 2	protein	773	38% helix, 17% strand	P19491

Ligands and binding sites

6ZP · 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	889	0.82	0.84	111	empty
2	1186	0.81	0.82	90	empty
3	945	0.81	0.82	109	6ZP
4	632	0.78	0.84	72	empty
5	824	0.76	0.80	82	6ZP

Interfaces

6 interfaces between chains.

A–B · 3842 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 3501 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 3025 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 3007 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 394 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation, glycation).

Compared structures

5L1F · AMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00

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 5L1F · PDBe 5L1F · UniProt P19491

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