MolNFT v1 · #107171 · protein

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

4U1W · Glutamate receptor 2: “Full length GLUA2-kainate-(R,R)-2B complex crystal form a”. X-ray diffraction, 3 ligands (KAI, FWF, NAG), 20 pockets (best druggability 0.80). MolNFT v1 #107171 on GenesisL1: 3D structure, binding sites and…

PDB: 4U1W
Type: protein
Length: 2,968 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 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate receptor 2	protein	731	43% helix, 19% strand	P19491
B	Glutamate receptor 2	protein	751	43% helix, 19% strand	P19491
C	Glutamate receptor 2	protein	736	43% helix, 19% strand	P19491
D	Glutamate receptor 2	protein	750	42% helix, 19% 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 A, D, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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	980	0.80	0.82	105	KAI, FWF
2	629	0.79	0.84	52	empty
3	1017	0.79	0.81	107	empty
4	883	0.77	0.80	83	FWF
5	910	0.77	0.80	92	empty

Interfaces

6 interfaces between chains.

C–D · 2946 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2904 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2451 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 2219 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 429 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4U1W · Full length GluA2-kainate-(R,R)-2b complex crystal form A · the same entry in another collection · chain C against C, 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 4U1W · PDBe 4U1W · UniProt P19491

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