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Structure of GLUK2-lbd in complex with gluazo

Analyse Structure of GLUK2-lbd in complex with gluazo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4H8I
Type: protein
Length: 512 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor, ionotropic kainate 2
UniProt: P42260
Ligands: 11W, CL, SO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glutamate receptor, ionotropic kainate 2	protein	256	39% helix, 22% strand	P42260

Ligands and binding sites

11W · (4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid · ligand · chains A
CL · Chloride ion · ion · chains A, B
SO4 · Sulfate ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B

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

Pockets

4 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	1187	0.77	0.79	108	MES
2	170	0.64	0.85	31	11W
3	156	0.54	0.81	28	empty
4	75	0.33	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 1020 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4H8I · Structure of GluK2-LBD in complex with GluAzo · the same entry in another collection · chain B against B, TM-score 1.00
P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · 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 P42260
Elsewhere: RCSB PDB 4H8I · PDBe 4H8I · UniProt P42260

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