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Cryo-EM structure of the BOC5-bound hglp-1R-gs complex

Analyse Cryo-EM structure of the BOC5-bound hglp-1R-gs complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7X8R
Type: protein
Length: 1,051 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
UniProt: P63092, P54311, P59768, P43220
Ligands: BYI
Pockets: 9 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	234	47% helix, 18% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 47% strand	P54311
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	53% helix, 0% strand	P59768
N	Nanobody 35	protein	126	7% helix, 44% strand	—
R	Glucagon-like peptide 1 receptor	protein	298	84% helix, 0% strand	P43220

Ligands and binding sites

BYI · 2,4-bis(3-methoxy-4-thiophen-2-ylcarbonyloxy-phenyl)-1, 3-bis[[4-[(2-methylpropan-2-yl) oxycarbonylamino]phenyl]carbonylamino]cyclobutane-1,3-dicarboxylic acid · ligand · chains R

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.84	0.85	78	empty
2	918	0.76	0.79	62	empty
3	819	0.74	0.78	67	BYI
4	883	0.73	0.78	80	empty
5	707	0.73	0.79	84	empty

Interfaces

6 interfaces between chains.

B–G · 2189 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1462 Å² buried · 32 hydrogen bonds · protein-protein
A–R · 1126 Å² buried · 12 hydrogen bonds · protein-protein
A–N · 760 Å² buried · 15 hydrogen bonds · protein-protein
B–N · 576 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7X8R · Cryo-EM structure of the Boc5-bound hGLP-1R-Gs complex · the same entry in another collection · chain G against G, TM-score 1.00
P54311 · 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 1.00
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 0.96
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 0.91

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 P63092
Every structure of UniProt P54311
Every structure of UniProt P59768
Every structure of UniProt P43220
Elsewhere: RCSB PDB 7X8R · PDBe 7X8R · UniProt P63092 · UniProt P54311 · UniProt P59768 · UniProt P43220

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