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Cryo-EM structure of the glucagon-like peptide-1 receptor in complex with G protein, glp-1 peptide and a positive allosteric modulator

Analyse Cryo-EM structure of the glucagon-like peptide-1 receptor in complex with G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VCB
Type: protein
Length: 1,158 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucagon-like peptide 1 receptor; Glucagon-like peptide 1; Guanine nucleotide-binding…
UniProt: P43220, P01275, P63092, P62873, P59768
Ligands: QW7
Pockets: 14 · best druggability 0.79

Structure

electron microscopy · 6 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Glucagon-like peptide 1 receptor	protein	378	63% helix, 4% strand	P43220
P	Glucagon-like peptide 1	protein	31	81% helix, 0% strand	P01275
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	223	46% helix, 15% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	7% helix, 45% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	59	54% helix, 0% strand	P59768
N	Nanobody 35	protein	128	7% helix, 41% strand	—

Ligands and binding sites

QW7 · 1-[(1R)-1-(2,6-dichloro-3-methoxyphenyl)ethyl]-6-{2-[(2R)-piperidin-2-yl]phenyl}-1H-benzimidazole · ligand · chains R, P

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	529	0.79	0.86	51	empty
2	948	0.79	0.81	74	empty
3	859	0.78	0.81	63	empty
4	131	0.68	0.90	26	empty
5	295	0.62	0.79	46	empty

Interfaces

7 interfaces between chains.

B–G · 2289 Å² buried · 15 hydrogen bonds · protein-protein
R–P · 1755 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1515 Å² buried · 20 hydrogen bonds · protein-protein
R–A · 1108 Å² buried · 14 hydrogen bonds · protein-protein
A–N · 895 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6VCB · Cryo-EM structure of the Glucagon-like peptide-1 receptor in complex with G protein… · the same entry in another collection · chain N against N, 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 0.99
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.90
P43220 · AlphaFold monomer V2.0 prediction for glucagon-like peptide 1 receptor (P43220) · a predicted model of the same protein · chain R against A, TM-score 0.84
P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.84
P01275 · AlphaFold monomer V2.0 prediction for pro-glucagon (P01275) · a predicted model of the same protein · chain P against A, TM-score 0.75

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 P43220
Every structure of UniProt P01275
Every structure of UniProt P63092
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 6VCB · PDBe 6VCB · UniProt P43220 · UniProt P01275 · UniProt P63092 · UniProt P62873 · UniProt P59768

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