Research workbench
Structural basis for the tethered peptide activation of adhesion gpcrs
Analyse Structural basis for the tethered peptide activation of adhesion gpcrs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EPT
- Type
- protein
- Length
- 1,009 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P62873, P59768, Q6QNK2
- Ligands
- PLM
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 213 | 46% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 62% helix, 0% strand | P59768 |
| N | Nanobody-35 | protein | 126 | 2% helix, 44% strand | — |
| R | Adhesion G-protein coupled receptor D1 | protein | 272 | 74% helix, 0% strand | Q6QNK2 |
Ligands and binding sites
- PLM · Palmitic acid · 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 | 781 | 0.84 | 0.87 | 76 | empty |
| 2 | 1029 | 0.80 | 0.82 | 85 | empty |
| 3 | 958 | 0.74 | 0.77 | 58 | empty |
| 4 | 176 | 0.66 | 0.86 | 24 | empty |
| 5 | 262 | 0.57 | 0.78 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2283 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1518 Ų buried · 15 hydrogen bonds · protein-protein
- A–R · 1122 Ų buried · 11 hydrogen bonds · protein-protein
- A–N · 758 Ų buried · 5 hydrogen bonds · protein-protein
- B–N · 463 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EPT · Structural basis for the tethered peptide activation of adhesion GPCRs · 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 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 G against A, TM-score 0.93
- Q6QNK2 · AlphaFold monomer V2.0 prediction for adhesion G-protein coupled receptor D1 (Q6QNK2) · a predicted model of the same protein · chain R against A, TM-score 0.93
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q6QNK2
- Elsewhere: RCSB PDB 7EPT · PDBe 7EPT · UniProt P62873 · UniProt P59768 · UniProt Q6QNK2
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