MolNFT v1 · #107172 · protein

Full length GLUA2-kainate-(R,R)-2B complex crystal form B

4U1X · Glutamate receptor 2: “Full length GLUA2-kainate-(R,R)-2B complex crystal form B”. X-ray diffraction, 3 ligands (KAI, FWF, NAG), 20 pockets (best druggability 0.84). MolNFT v1 #107172 on GenesisL1: 3D structure, binding sites and…

PDB: 4U1X
Type: protein
Length: 2,980 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2
UniProt: P19491
Ligands: KAI, FWF, NAG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor 2	protein	743	41% helix, 19% strand	P19491
B	Glutamate receptor 2	protein	738	41% helix, 17% strand	P19491
C	Glutamate receptor 2	protein	755	42% helix, 18% strand	P19491
D	Glutamate receptor 2	protein	744	42% helix, 18% strand	P19491

Ligands and binding sites

KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 4 copies · chains A, B, C, D
FWF · N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide · ligand · 2 copies · chains B, C, A, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B, 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	1074	0.84	0.85	132	KAI, FWF
2	1137	0.80	0.81	115	KAI, FWF
3	915	0.78	0.81	74	empty
4	1152	0.78	0.80	96	empty
5	920	0.77	0.80	85	empty

Interfaces

6 interfaces between chains.

C–D · 3595 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 3268 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2314 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 2073 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1096 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4U1X · Full length GluA2-kainate-(R,R)-2b complex crystal form B · 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 C against A, TM-score 0.85

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 4U1X · PDBe 4U1X · UniProt P19491

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