MolNFT v1 · #124949 · protein

GLUK2EM with 2S,4R-4-methylglutamate

5KUF · Glutamate receptor ionotropic, kainate 2: “GLUK2EM with 2S,4R-4-methylglutamate”. Electron microscopy, 1 ligand (SYM), 20 pockets (best druggability 0.82). MolNFT v1 #124949 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5KUF
Type: protein
Length: 3,000 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor ionotropic, kainate 2
UniProt: P42260
Ligands: SYM
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glutamate receptor ionotropic, kainate 2	protein	750	40% helix, 17% strand	P42260

Ligands and binding sites

SYM · 2S,4R-4-methylglutamate · ligand · 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	1144	0.82	0.84	129	empty
2	738	0.80	0.84	84	empty
3	1051	0.80	0.80	95	empty
4	782	0.74	0.79	82	empty
5	87	0.73	0.96	21	SYM

Interfaces

5 interfaces between chains.

C–D · 3137 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 3113 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1378 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 1374 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 631 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5KUF · GluK2EM with 2S,4R-4-methylglutamate · the same entry in another collection · chain C against C, 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 0.83

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 5KUF · PDBe 5KUF · UniProt P42260

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