Research workbench
Cryo-EM structure of SEW2871-bound Sphingosine-1-phosphate receptor 1 in complex with Gi protein
Analyse Cryo-EM structure of SEW2871-bound Sphingosine-1-phosphate receptor 1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EW7
- Type
- protein
- Length
- 1,144 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.27
- Source
- Homo sapiens; Mus musculus
- Molecule
- Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768
- Ligands
- JEX
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · resolution 3.27 · 5 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 228 | 41% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 36% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 57% helix, 0% strand | P59768 |
| D | Sphingosine 1-phosphate receptor 1 | protein | 286 | 76% helix, 1% strand | — |
| E | scFv16 | protein | 232 | 1% helix, 40% strand | — |
Ligands and binding sites
- JEX · 5-[4-phenyl-5-(trifluoromethyl)thiophen-2-yl]-3-[3-(trifluoromethyl)phenyl]-1,2,4-oxadiazole · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.82 | 0.84 | 64 | empty |
| 2 | 642 | 0.81 | 0.85 | 57 | JEX |
| 3 | 844 | 0.70 | 0.76 | 79 | empty |
| 4 | 101 | 0.58 | 0.86 | 19 | empty |
| 5 | 151 | 0.57 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2182 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1242 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1219 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 632 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 416 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EW7 · Cryo-EM structure of SEW2871-bound sphingosine-1-phosphate receptor 1 in complex with gi… · 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
- 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 0.80
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
- Elsewhere: RCSB PDB 7EW7 · PDBe 7EW7 · UniProt P63096 · UniProt P62873 · UniProt P59768
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