Research workbench
Structure of S1PR2-heterotrimeric G13 signaling complex
Analyse Structure of S1PR2-heterotrimeric G13 signaling complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T6B
- Type
- protein
- Length
- 1,119 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein subunit alpha-13; Guanine nucleotide-binding protein…
- UniProt
- Q14344, P62873, P59768, O95136
- Ligands
- S1P
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein subunit alpha-13 | protein | 225 | 38% helix, 14% strand | Q14344 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 6% helix, 46% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 51% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 3% helix, 46% strand | — |
| R | Sphingosine 1-phosphate receptor 2 | protein | 264 | 74% helix, 0% strand | O95136 |
Ligands and binding sites
- S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.84 | 0.87 | 56 | S1P |
| 2 | 751 | 0.83 | 0.86 | 56 | empty |
| 3 | 957 | 0.70 | 0.75 | 75 | empty |
| 4 | 453 | 0.65 | 0.78 | 64 | empty |
| 5 | 97 | 0.60 | 0.87 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2352 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 1045 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 582 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 382 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7T6B · Structure of S1PR2-heterotrimeric G13 signaling complex · the same entry in another collection · chain R against R, 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 0.99
- O95136 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 2 (O95136) · a predicted model of the same protein · chain R against A, TM-score 0.91
- 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 0.91
- Q14344 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit alpha-13… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 Q14344
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt O95136
- Elsewhere: RCSB PDB 7T6B · PDBe 7T6B · UniProt Q14344 · UniProt P62873 · UniProt P59768 · UniProt O95136
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