MolNFT v1 · #177853 · protein
Cryo-EM structure of ozanimod -bound sphingosine-1-phosphate receptor 1 in complex with gi protein
7EW0 · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of ozanimod -bound sphingosine-1-phosphate receptor 1 in complex with gi protein”. Electron microscopy, 1 ligand (JEU), 15 pockets (best druggability 0.82).…
- PDB
- 7EW0
- Type
- protein
- Length
- 1,142 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
- JEU
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 228 | 41% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 38% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 55% helix, 0% strand | P59768 |
| D | Sphingosine 1-phosphate receptor 1 | protein | 284 | 76% helix, 1% strand | — |
| E | SCFV16 | protein | 232 | 1% helix, 41% strand | — |
Ligands and binding sites
- JEU · 5-[3-[(1~{S})-1-(2-hydroxyethylamino)-2,3-dihydro-1~{H}-inden-4-yl]-1,2,4-oxadiazol-5-yl]-2-propan-2-yloxy-benzenecarbonitrile · 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 | 1023 | 0.82 | 0.83 | 70 | empty |
| 2 | 457 | 0.81 | 0.88 | 45 | JEU |
| 3 | 909 | 0.71 | 0.76 | 69 | empty |
| 4 | 77 | 0.59 | 0.89 | 18 | empty |
| 5 | 114 | 0.53 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2249 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1343 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1207 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 574 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 427 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EW0 · Cryo-EM structure of ozanimod -bound Sphingosine-1-phosphate receptor 1 in complex with… · the same entry in another collection · chain D against D, 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 7EW0 · PDBe 7EW0 · UniProt P63096 · UniProt P62873 · UniProt P59768
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