Research workbench
Lysophosphatidic acid receptor 1-gi complex bound to lpa, state a
Analyse Lysophosphatidic acid receptor 1-gi complex bound to lpa, state a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TD1
- Type
- protein
- Length
- 906 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysophosphatidic acid receptor 1; Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
- UniProt
- Q92633, P62871, B2RSH2, P63212
- Ligands
- NKP
- Pockets
- 8 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Lysophosphatidic acid receptor 1 | protein | 293 | 73% helix, 0% strand | Q92633 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62871 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 45% helix, 20% strand | B2RSH2 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P63212 |
Ligands and binding sites
- NKP · (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.82 | 0.88 | 53 | NKP |
| 2 | 837 | 0.82 | 0.84 | 65 | empty |
| 3 | 665 | 0.69 | 0.77 | 67 | empty |
| 4 | 120 | 0.47 | 0.79 | 24 | empty |
| 5 | 174 | 0.43 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–G · 2043 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1177 Ų buried · 12 hydrogen bonds · protein-protein
- R–A · 1097 Ų buried · 2 hydrogen bonds · protein-protein
- R–B · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7TD1 · Lysophosphatidic acid receptor 1-Gi complex bound to LPA, state a · the same entry in another collection · chain G against G, 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 0.99
- Q92633 · AlphaFold monomer V2.0 prediction for lysophosphatidic acid receptor 1 (Q92633) · 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 0.72
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 Q92633
- Every structure of UniProt P62871
- Every structure of UniProt B2RSH2
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7TD1 · PDBe 7TD1 · UniProt Q92633 · UniProt P62871 · UniProt B2RSH2 · UniProt P63212
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