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Piracetam bound to the ligand binding domain of GLUA2 (flop form)

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

PDB: 3LSL
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: 6 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	Glutamate receptor 2	protein	258	38% helix, 21% strand	P19491

Ligands and binding sites

PZI · 2-(2-oxopyrrolidin-1-yl)acetamide · ligand · 9 copies · chains A, D, G
GLU · Glutamic acid · ligand · 3 copies · chains A, D, G
ZN · Zinc ion · metal · 5 copies · chains A, D, G

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

Pockets

6 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	976	0.83	0.84	123	PZI
2	266	0.58	0.78	29	empty
3	270	0.53	0.75	40	empty
4	92	0.41	0.78	24	empty
5	108	0.40	0.75	25	empty

Interfaces

3 interfaces between chains.

A–D · 983 Å² buried · 11 hydrogen bonds · protein-protein
D–G · 294 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 79 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3LSL · Piracetam bound to the ligand binding domain of GluA2 (flop form) · 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 D 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 3LSL · PDBe 3LSL · UniProt P19491

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