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Crystal titration experiment (AMPA complex control)

Analyse Crystal titration experiment (AMPA complex control) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MY2
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: AMQ, ZN
Pockets: 9 · best druggability 0.78

Structure

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

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

Ligands and binding sites

AMQ · (S)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid · ligand · 3 copies · chains A, B, 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

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	569	0.78	0.85	91	empty
2	60	0.74	0.99	20	AMQ
3	59	0.73	0.99	19	AMQ
4	55	0.71	0.98	18	AMQ
5	624	0.70	0.78	49	empty

Interfaces

3 interfaces between chains.

A–C · 1022 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 273 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 111 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1MY2 · crystal titration experiment (AMPA complex control) · 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 1MY2 · PDBe 1MY2 · UniProt P19491

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