Research workbench
Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 5 in complex with Gi protein
Analyse Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 5 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EW1
- Type
- protein
- Length
- 1,129 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Guanine…
- UniProt
- P62873, P59768, P63096, Q9H228
- Ligands
- J8C
- Pockets
- 15 · best druggability 0.85
Structure
electron microscopy · resolution 3.4 · 5 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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 | 51% helix, 0% strand | P59768 |
| D | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 227 | 38% helix, 15% strand | P63096 |
| E | scFv16 | protein | 232 | 0% helix, 44% strand | — |
| A | Sphingosine 1-phosphate receptor 5 | protein | 269 | 73% helix, 1% strand | Q9H228 |
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
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.85 | 0.87 | 66 | J8C |
| 2 | 989 | 0.83 | 0.84 | 67 | empty |
| 3 | 63 | 0.69 | 0.95 | 22 | empty |
| 4 | 610 | 0.67 | 0.77 | 50 | empty |
| 5 | 356 | 0.62 | 0.78 | 47 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2253 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1131 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 1028 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 566 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 445 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EW1 · Cryo-EM structure of siponimod -bound sphingosine-1-phosphate receptor 5 in complex with… · 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 B against A, TM-score 0.99
- Q9H228 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 5 (Q9H228) · a predicted model of the same protein · chain A against A, TM-score 0.91
- 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 0.84
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain D 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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P63096
- Every structure of UniProt Q9H228
- Elsewhere: RCSB PDB 7EW1 · PDBe 7EW1 · UniProt P62873 · UniProt P59768 · UniProt P63096 · UniProt Q9H228
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