Research workbench
Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to FTY720P
Analyse Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to FTY720P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EO2
- Type
- protein
- Length
- 1,126 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
- J89
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine 1-phosphate receptor 1 | protein | 280 | 74% helix, 1% strand | P21453 |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 220 | 44% helix, 19% strand | P63096 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 45% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 66% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 231 | 3% helix, 49% strand | — |
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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.83 | 0.84 | 64 | empty |
| 2 | 596 | 0.81 | 0.86 | 50 | J89 |
| 3 | 584 | 0.69 | 0.78 | 67 | empty |
| 4 | 675 | 0.66 | 0.75 | 61 | empty |
| 5 | 359 | 0.57 | 0.75 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2150 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1106 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 888 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 546 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 410 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EO2 · Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to FTY720p · 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 0.88
- 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 0.81
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 7EO2 · PDBe 7EO2 · 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.