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Cryo-EM structure of pFTY720-bound Sphingosine 1-phosphate receptor 3 in complex with Gi protein

Analyse Cryo-EM structure of pFTY720-bound Sphingosine 1-phosphate receptor 3 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EW2
Type: protein
Length: 1,149 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.1
Source: Homo sapiens
Molecule: Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, Q99500
Ligands: J89
Pockets: 13 · best druggability 0.81

Structure

electron microscopy · resolution 3.1 · 5 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(i) subunit alpha-1	protein	226	40% helix, 16% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	340	8% helix, 42% strand	P62873
C	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	61	54% helix, 0% strand	P59768
S	scFV16	protein	232	4% helix, 47% strand	—
R	Sphingosine 1-phosphate receptor 3	protein	290	74% helix, 0% strand	Q99500

Ligands and binding sites

J89 · (2~{S})-2-azanyl-4-(4-octylphenyl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]butan-1-ol · ligand · 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	902	0.81	0.83	66	empty
2	595	0.81	0.86	59	J89
3	963	0.71	0.75	67	empty
4	389	0.61	0.77	45	empty
5	185	0.56	0.80	31	empty

Interfaces

6 interfaces between chains.

B–C · 2182 Å² buried · 20 hydrogen bonds · protein-protein
A–R · 1401 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1187 Å² buried · 13 hydrogen bonds · protein-protein
A–S · 609 Å² buried · 3 hydrogen bonds · protein-protein
B–S · 450 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7EW2 · Cryo-EM structure of PFTY720-bound sphingosine 1-phosphate receptor 3 in complex with gi… · the same entry in another collection · chain S against S, 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
Q99500 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 3 (Q99500) · 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 C 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 0.82

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 Q99500
Elsewhere: RCSB PDB 7EW2 · PDBe 7EW2 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q99500

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