Research workbench
Sphingosine-1-phosphate receptor 1-gi complex bound to siponimod
Analyse Sphingosine-1-phosphate receptor 1-gi complex bound to siponimod in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TD4
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Guanine…
- UniProt
- P62871, B2RSH2, P63212, P21453
- Ligands
- J8C, NAG
- Pockets
- 6 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 331 | 5% helix, 49% strand | P62871 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 222 | 45% helix, 18% strand | B2RSH2 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 59% helix, 0% strand | P63212 |
| R | Sphingosine 1-phosphate receptor 1 | protein | 290 | 73% helix, 1% strand | P21453 |
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 R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.85 | 69 | empty |
| 2 | 440 | 0.79 | 0.87 | 46 | J8C |
| 3 | 582 | 0.65 | 0.76 | 55 | empty |
| 4 | 190 | 0.49 | 0.76 | 26 | empty |
| 5 | 60 | 0.35 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–G · 1975 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1203 Ų buried · 15 hydrogen bonds · protein-protein
- A–R · 1118 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TD4 · Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod · the same entry in another collection · chain R against R, TM-score 1.00
- P62871 · 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 1.00
- P21453 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 1 (P21453) · a predicted model of the same protein · chain R against A, TM-score 0.93
- B2RSH2 · 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 0.82
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.64
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 P62871
- Every structure of UniProt B2RSH2
- Every structure of UniProt P63212
- Every structure of UniProt P21453
- Elsewhere: RCSB PDB 7TD4 · PDBe 7TD4 · UniProt P62871 · UniProt B2RSH2 · UniProt P63212 · UniProt P21453
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