MolNFT v1 · #177615 · protein
Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to BAF312
7EO4: “Cryo-EM of sphingosine 1-phosphate receptor 1 / gi complex bound to BAF312”. Electron microscopy, 1 ligand (J8C), 17 pockets (best druggability 0.83). MolNFT v1 #177615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EO4
- Type
- protein
- Length
- 1,059 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine 1-phosphate receptor 1; Guanine nucleotide-binding protein G(I) subunit…
- UniProt
- P21453, P63096, P62873, P59768
- Ligands
- J8C
- Pockets
- 17 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine 1-phosphate receptor 1 | protein | 282 | 73% helix, 0% strand | P21453 |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 151 | 34% helix, 16% strand | P63096 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 64% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 231 | 3% helix, 51% 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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.83 | 0.84 | 68 | empty |
| 2 | 796 | 0.82 | 0.85 | 58 | J8C |
| 3 | 609 | 0.69 | 0.78 | 73 | empty |
| 4 | 85 | 0.68 | 0.93 | 19 | empty |
| 5 | 782 | 0.67 | 0.75 | 62 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2077 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1032 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 546 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 383 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7EO4 · Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312 · 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 C against A, TM-score 0.98
- P21453 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 1 (P21453) · a predicted model of the same protein · chain A against A, TM-score 0.92
- 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 D against A, TM-score 0.81
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.71
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 P21453
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7EO4 · PDBe 7EO4 · UniProt P21453 · UniProt P63096 · UniProt P62873 · UniProt P59768
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