MolNFT v1 · #177851 · protein
Cryo-EM structure of siponimod -bound sphingosine-1-phosphate receptor 1 in complex with gi protein
7EVY · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of siponimod -bound sphingosine-1-phosphate receptor 1 in complex with gi protein”. Electron microscopy, 2 ligands (J8C, NAG), 12 pockets (best druggability…
- PDB
- 7EVY
- 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
- J8C, NAG
- Pockets
- 12 · best druggability 0.82
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, 40% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 50% helix, 0% strand | P59768 |
| D | Sphingosine 1-phosphate receptor 1 | protein | 286 | 73% helix, 1% strand | — |
| E | SCFV16 | protein | 232 | 3% helix, 43% strand | — |
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 D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.82 | 0.83 | 65 | empty |
| 2 | 588 | 0.80 | 0.85 | 48 | J8C |
| 3 | 1066 | 0.72 | 0.76 | 86 | empty |
| 4 | 418 | 0.67 | 0.80 | 62 | empty |
| 5 | 194 | 0.52 | 0.78 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2290 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1432 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1211 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 625 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 415 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7EVY · Cryo-EM structure of siponimod -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 0.88
- 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 7EVY · PDBe 7EVY · UniProt P63096 · UniProt P62873 · UniProt P59768
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