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Piracetam bound to the ligand binding domain of GLUA2

Analyse Piracetam bound to the ligand binding domain of GLUA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LSF
Type: protein
Length: 774 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: PZI, GLU, ZN
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E, H	Glutamate receptor 2	protein	258	39% helix, 21% strand	P19491

Ligands and binding sites

PZI · 2-(2-oxopyrrolidin-1-yl)acetamide · ligand · 6 copies · chains B, E, H
GLU · Glutamic acid · ligand · 3 copies · chains B, E, H
ZN · Zinc ion · metal · 5 copies · chains E, B, H

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

Pockets

7 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	1024	0.82	0.83	131	PZI
2	285	0.58	0.78	32	empty
3	164	0.44	0.75	27	empty
4	100	0.37	0.75	23	empty
5	108	0.35	0.73	19	empty

Interfaces

3 interfaces between chains.

B–E · 939 Å² buried · 8 hydrogen bonds · protein-protein
B–H · 224 Å² buried · 5 hydrogen bonds · protein-protein
E–H · 69 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3LSF · Piracetam bound to the ligand binding domain of GluA2 · the same entry in another collection · chain B against B, TM-score 1.00
P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B 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 3LSF · PDBe 3LSF · UniProt P19491

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