Research workbench
Cryo-EM structure of cenerimod -bound sphingosine-1-phosphate receptor 1 in complex with gi protein
Analyse Cryo-EM structure of cenerimod -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
- 7EVZ
- Type
- protein
- Length
- 1,144 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768
- Ligands
- PLM, JER
- Pockets
- 15 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 228 | 40% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 39% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 52% helix, 0% strand | P59768 |
| D | Sphingosine 1-phosphate receptor 1 | protein | 286 | 76% helix, 1% strand | — |
| E | SCFV16 | protein | 232 | 1% helix, 43% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains D
- JER · (2~{S})-3-[4-[5-(2-cyclopentyl-6-methoxy-pyridin-4-yl)-1,2,4-oxadiazol-3-yl]-2-ethyl-6-methyl-phenoxy]propane-1,2-diol · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.83 | 0.89 | 42 | JER |
| 2 | 885 | 0.82 | 0.84 | 60 | empty |
| 3 | 864 | 0.72 | 0.77 | 63 | empty |
| 4 | 251 | 0.62 | 0.81 | 36 | empty |
| 5 | 198 | 0.55 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2349 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1466 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1200 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 584 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 430 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EVZ · Cryo-EM structure of cenerimod -bound Sphingosine-1-phosphate receptor 1 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
- 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 0.90
- 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
- Elsewhere: RCSB PDB 7EVZ · PDBe 7EVZ · UniProt P63096 · UniProt P62873 · UniProt P59768
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