MolNFT v1 · #182962 · protein

Structures of human ghrelin receptor-gi complexes with ghrelin and a synthetic agonist

7NA7 · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Structures of human ghrelin receptor-gi complexes with ghrelin and a synthetic agonist”. Electron microscopy, 1 ligand (CLR), 13 pockets (best druggability 0.82). MolNFT v1…

PDB: 7NA7
Type: protein
Length: 1,142 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, Q92847, Q9UBU3
Ligands: CLR
Pockets: 13 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	217	43% helix, 18% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	336	5% helix, 47% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	54	50% helix, 0% strand	P59768
N	Antibody fragment	protein	232	3% helix, 48% strand	—
R	Growth hormone secretagogue receptor type 1	protein	291	82% helix, 1% strand	Q92847
L	Ghrelin-27	protein	12	0% helix, 0% strand	Q9UBU3

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains R

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	747	0.82	0.85	65	empty
2	961	0.79	0.81	74	empty
3	268	0.59	0.79	43	empty
4	168	0.52	0.79	22	empty
5	108	0.50	0.82	25	empty

Interfaces

7 interfaces between chains.

B–G · 2186 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1153 Å² buried · 14 hydrogen bonds · protein-protein
A–R · 1104 Å² buried · 4 hydrogen bonds · protein-protein
R–L · 1017 Å² buried · 12 hydrogen bonds · protein-protein
A–N · 569 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

7NA7 · Structures of human ghrelin receptor-Gi complexes with ghrelin and a synthetic agonist · the same entry in another collection · chain L against L, 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 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 0.94
Q92847 · AlphaFold monomer V2.0 prediction for growth hormone secretagogue receptor type 1 (Q92847) · a predicted model of the same protein · chain R against A, TM-score 0.94
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
Q9UBU3 · AlphaFold monomer V2.0 prediction for appetite-regulating hormone (Q9UBU3) · a predicted model of the same protein · chain L against A, TM-score 0.27

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 P63096
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt Q92847
Every structure of UniProt Q9UBU3
Elsewhere: RCSB PDB 7NA7 · PDBe 7NA7 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q92847 · UniProt Q9UBU3

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