MolNFT v2 · #179127 · protein

Apo serotonin 1A (5-HT1A) receptor-Gi protein complex

7E2X · Guanine nucleotide-binding protein G(i) subunit alpha-1: “Apo serotonin 1A (5-HT1A) receptor-Gi protein complex”. Electron microscopy at 3.0, 3 ligands (CLR, PLM, J40), 10 pockets (best druggability 0.84). MolNFT v2 #179127 on…

PDB: 7E2X
Type: protein
Length: 870 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.0
Source: Escherichia coli; Homo sapiens
Molecule: Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, P0ABE7, P08908
Ligands: CLR, PLM, J40
Pockets: 10 · best druggability 0.84

Structure

electron microscopy · resolution 3.0 · 4 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(i) subunit alpha-1	protein	219	46% helix, 17% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	328	5% helix, 47% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	45	49% helix, 0% strand	P59768
R	Soluble cytochrome b562,5-hydroxytryptamine receptor 1A	protein	278	86% helix, 0% strand	P0ABE7, P08908

Ligands and binding sites

CLR · Cholesterol · ligand · 10 copies · chains R
PLM · Palmitic acid · ligand · 3 copies · chains R
J40 · [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E, 8E)-hexadeca-5,8,11,14-tetraenoate · ligand · chains A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.84	0.85	69	empty
2	463	0.75	0.84	41	empty
3	1156	0.72	0.76	92	empty
4	255	0.59	0.79	33	empty
5	92	0.45	0.80	19	empty

Interfaces

4 interfaces between chains.

B–G · 1956 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1206 Å² buried · 7 hydrogen bonds · protein-protein
A–R · 1170 Å² buried · 6 hydrogen bonds · protein-protein
B–R · 111 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7E2X · Apo serotonin 1A (5-HT1A) receptor-gi protein complex · the same entry in another collection · chain A against A, 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
P08908 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 1A (P08908) · a predicted model of the same protein · chain R against A, TM-score 0.89
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 0.85
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 0.79
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain R 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 P0ABE7
Every structure of UniProt P08908
Elsewhere: RCSB PDB 7E2X · PDBe 7E2X · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P0ABE7 · UniProt P08908

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