Research workbench
Cryo-EM structure of CYM-5541-bound Sphingosine 1-phosphate receptor 3 in complex with Gi protein
Analyse Cryo-EM structure of CYM-5541-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
- 7EW4
- Type
- protein
- Length
- 1,145 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens
- Molecule
- Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, Q99500
- Ligands
- PLM, JF9
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · resolution 3.2 · 5 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 228 | 46% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 9% helix, 45% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 48% helix, 0% strand | P59768 |
| R | Sphingosine 1-phosphate receptor 3 | protein | 287 | 77% helix, 1% strand | Q99500 |
| S | scFV16 | protein | 232 | 4% helix, 44% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains R
- JF9 · N,N-dicyclohexyl-5-cyclopropyl-1,2-oxazole-3-carboxamide · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.82 | 0.84 | 69 | empty |
| 2 | 639 | 0.79 | 0.84 | 64 | JF9 |
| 3 | 957 | 0.74 | 0.77 | 97 | empty |
| 4 | 218 | 0.58 | 0.80 | 32 | empty |
| 5 | 258 | 0.56 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2098 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 1348 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 12 hydrogen bonds · protein-protein
- A–S · 561 Ų buried · 8 hydrogen bonds · protein-protein
- B–S · 441 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EW4 · Cryo-EM structure of cym-5541-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 0.98
- 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 0.90
- 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 A 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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q99500
- Elsewhere: RCSB PDB 7EW4 · PDBe 7EW4 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q99500
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