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Cryo-EM structure of the ghrelin-bound human ghrelin receptor-go complex

Analyse Cryo-EM structure of the ghrelin-bound human ghrelin receptor-go complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7W2Z
Type: protein
Length: 1,154 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(O) subunit alpha; Growth hormone secretagogue…
UniProt: A0A1W2PS82, P09471, Q92847, P59768, P62873, Q9UBU3
Ligands: CLR, K4Q
Pockets: 15 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(O) subunit alpha	protein	213	41% helix, 17% strand	A0A1W2PS82, P09471
R	Growth hormone secretagogue receptor type 1	protein	301	70% helix, 3% strand	Q92847
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	45% helix, 0% strand	P59768
S	SCFV16	protein	232	4% helix, 48% strand	—
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	7% helix, 47% strand	P62873
L	Appetite-regulating hormone	protein	15	33% helix, 0% strand	Q9UBU3

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains R
K4Q · [(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate · ligand · chains R, L

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.82	0.85	61	empty
2	161	0.81	0.96	21	K4Q
3	1192	0.71	0.75	99	CLR
4	120	0.64	0.88	23	empty
5	102	0.60	0.87	24	empty

Interfaces

7 interfaces between chains.

G–B · 2098 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1161 Å² buried · 17 hydrogen bonds · protein-protein
R–L · 969 Å² buried · 8 hydrogen bonds · protein-protein
A–R · 957 Å² buried · 4 hydrogen bonds · protein-protein
A–S · 577 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

7W2Z · Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex · 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 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 0.93
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 0.92
P09471 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(O) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.76
Q9UBU3 · AlphaFold monomer V2.0 prediction for appetite-regulating hormone (Q9UBU3) · a predicted model of the same protein · chain L against A, TM-score 0.40

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 A0A1W2PS82
Every structure of UniProt P09471
Every structure of UniProt Q92847
Every structure of UniProt P59768
Every structure of UniProt P62873
Every structure of UniProt Q9UBU3
Elsewhere: RCSB PDB 7W2Z · PDBe 7W2Z · UniProt A0A1W2PS82 · UniProt P09471 · UniProt Q92847 · UniProt P59768 · UniProt P62873 · UniProt Q9UBU3

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