Research workbench

Cryo-EM structure of gi-bound metabotropic glutamate receptor MGLU2

Analyse Cryo-EM structure of gi-bound metabotropic glutamate receptor MGLU2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E9G
Type: protein
Length: 2,557 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metabotropic glutamate receptor 2; Guanine nucleotide-binding protein G(I) subunit…
UniProt: Q14416, P63096, P62873, P59768
Ligands: 40F, HZR
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 7 distinct chains · 31% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Metabotropic glutamate receptor 2	protein	769	43% helix, 10% strand	Q14416
S	Metabotropic glutamate receptor 2	protein	755	43% helix, 10% strand	Q14416
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	223	36% helix, 19% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	311	1% helix, 39% strand	P62873
C	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	33	42% helix, 0% strand	P59768
D	SCFV16	protein	232	1% helix, 35% strand	—
E, F	DN13	protein	117	0% helix, 38% strand	—

Ligands and binding sites

40F · (1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid · ligand · 2 copies · chains R, S
HZR · 1-butyl-3-chloranyl-4-(4-phenylpiperidin-1-yl)pyridin-2-one · ligand · chains R

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	913	0.88	0.90	91	empty
2	783	0.82	0.85	70	empty
3	1095	0.80	0.81	83	HZR
4	163	0.75	0.92	34	empty
5	75	0.75	0.99	24	40F

Interfaces

10 interfaces between chains.

R–S · 1718 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 1171 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 1080 Å² buried · 5 hydrogen bonds · protein-protein
R–E · 944 Å² buried · 15 hydrogen bonds · protein-protein
S–F · 939 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

7E9G · Cryo-EM structure of Gi-bound metabotropic glutamate receptor mGlu2 · the same entry in another collection · chain F against F, TM-score 1.00
P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.98
Q14416 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 2 (Q14416) · a predicted model of the same protein · chain S against A, TM-score 0.84
P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82

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 Q14416
Every structure of UniProt P63096
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7E9G · PDBe 7E9G · UniProt Q14416 · UniProt P63096 · UniProt P62873 · UniProt P59768

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