Research workbench

Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to BAF312

Analyse Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to BAF312 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EO4
Type: protein
Length: 1,059 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sphingosine 1-phosphate receptor 1; Guanine nucleotide-binding protein G(I) subunit…
UniProt: P21453, P63096, P62873, P59768
Ligands: J8C
Pockets: 17 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sphingosine 1-phosphate receptor 1	protein	282	73% helix, 0% strand	P21453
B	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	151	34% helix, 16% strand	P63096
C	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 45% strand	P62873
D	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	56	64% helix, 0% strand	P59768
E	SCFV16	protein	231	3% helix, 51% strand	—

Ligands and binding sites

J8C · 1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl) phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid · ligand · chains A

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

Pockets

17 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	990	0.83	0.84	68	empty
2	796	0.82	0.85	58	J8C
3	609	0.69	0.78	73	empty
4	85	0.68	0.93	19	empty
5	782	0.67	0.75	62	empty

Interfaces

6 interfaces between chains.

C–D · 2077 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1032 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1016 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 546 Å² buried · 3 hydrogen bonds · protein-protein
C–E · 383 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7EO4 · Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312 · the same entry in another collection · chain E against E, 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 C against A, TM-score 0.98
P21453 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 1 (P21453) · a predicted model of the same protein · chain A 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 D against A, TM-score 0.81
P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.71

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 P21453
Every structure of UniProt P63096
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7EO4 · PDBe 7EO4 · UniProt P21453 · UniProt P63096 · UniProt P62873 · UniProt P59768

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.