Research workbench

Lasmiditan-bound serotonin 1F (5-HT1F) receptor-Gi protein complex

Analyse Lasmiditan-bound serotonin 1F (5-HT1F) receptor-Gi protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EXD
Type: protein
Length: 1,118 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Escherichia coli; Homo sapiens; Mus musculus
Molecule: Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, P0ABE7, P30939
Ligands: 05X
Pockets: 14 · best druggability 0.81

Structure

electron microscopy · resolution 3.4 · 5 distinct chains · 35% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(i) subunit alpha-1	protein	219	46% helix, 18% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	337	7% helix, 49% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	57% helix, 0% strand	P59768
E	scFv16	protein	232	4% helix, 49% strand	—
R	Soluble cytochrome b562,5-hydroxytryptamine receptor 1F	protein	272	81% helix, 0% strand	P0ABE7, P30939

Ligands and binding sites

05X · 2,4,6-tris(fluoranyl)-N-[6-(1-methylpiperidin-4-yl) carbonylpyridin-2-yl]benzamide · ligand · chains R

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

Pockets

14 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	663	0.81	0.85	66	empty
2	430	0.80	0.88	49	05X
3	1163	0.77	0.79	90	empty
4	98	0.74	0.95	31	empty
5	213	0.60	0.82	30	empty

Interfaces

6 interfaces between chains.

B–G · 2212 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1245 Å² buried · 12 hydrogen bonds · protein-protein
A–R · 938 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 555 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 470 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7EXD · Lasmiditan-bound serotonin 1F (5-HT1F) receptor-gi protein 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
P30939 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 1F (P30939) · a predicted model of the same protein · chain R against A, TM-score 0.92
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 0.92
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 0.81
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain R against A, TM-score 0.28

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 P30939
Elsewhere: RCSB PDB 7EXD · PDBe 7EXD · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P0ABE7 · UniProt P30939

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