MolNFT v1 · #175079 · protein

Cryo-EM structure of the int-777-bound gpbar-gs complex

7CFN · Guanine nucleotide-binding protein G(S) subunit alpha…: “Cryo-EM structure of the int-777-bound gpbar-gs complex”. Electron microscopy, 3 ligands (FX0, CLR, PLM), 10 pockets (best druggability 0.83). MolNFT v1 #175079 on GenesisL1…

PDB: 7CFN
Type: protein
Length: 1,031 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, P62873, P59768, Q8TDU6
Ligands: FX0, CLR, PLM
Pockets: 10 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	232	47% helix, 18% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	9% helix, 45% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	59% helix, 0% strand	P59768
N	Nanobody-35	protein	128	2% helix, 38% strand	—
R	G-protein coupled bile acid receptor 1	protein	274	77% helix, 0% strand	Q8TDU6

Ligands and binding sites

FX0 · (2S,4R)-4-[(3R,5S,6R,7R,8R,9S,10S,12S,13R,14S,17R)-6-ethyl-10,13-dimethyl-3,7,12-tris(oxidanyl)-2,3,4,5,6, 7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methyl-pentanoic acid · ligand · 2 copies · chains R
CLR · Cholesterol · ligand · chains R
PLM · Palmitic acid · ligand · chains R

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.83	0.86	79	empty
2	484	0.79	0.86	33	FX0
3	894	0.76	0.79	60	empty
4	354	0.75	0.86	33	empty
5	983	0.72	0.76	69	empty

Interfaces

6 interfaces between chains.

B–G · 2209 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1466 Å² buried · 15 hydrogen bonds · protein-protein
A–R · 1398 Å² buried · 11 hydrogen bonds · protein-protein
A–N · 757 Å² buried · 8 hydrogen bonds · protein-protein
B–N · 605 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7CFN · Cryo-EM structure of the INT-777-bound GPBAR-Gs complex · the same entry in another collection · chain R against R, 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
Q8TDU6 · AlphaFold monomer V2.0 prediction for G-protein coupled bile acid receptor 1 (Q8TDU6) · a predicted model of the same protein · chain R against A, TM-score 0.95
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 0.93

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 P62873
Every structure of UniProt P59768
Every structure of UniProt Q8TDU6
Elsewhere: RCSB PDB 7CFN · PDBe 7CFN · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt Q8TDU6

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