Research workbench
Human Amylin1 Receptor in complex with Gs and rat amylin peptide
Analyse Human Amylin1 Receptor in complex with Gs and rat amylin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TYF
- Type
- protein
- Length
- 1,266 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens; Lama glama; SYNTHETIC CONSTRUCT
- Molecule
- Guanine nucleotide-binding protein G(s) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P62873, O60894, P59768, P12969, P30988
- Ligands
- PLM, Y01, P42, PTY, NAG
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · resolution 2.2 · 7 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 228 | 48% helix, 18% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 47% strand | P62873 |
| E | Receptor activity-modifying protein 1 | protein | 112 | 69% helix, 0% strand | O60894 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 58% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 45% strand | — |
| P | amylin peptide | protein | 37 | 38% helix, 3% strand | P12969 |
| R | Calcitonin receptor | protein | 367 | 68% helix, 7% strand | P30988 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 9 copies · chains R, E
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains R
- P42 · (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains P, R
- PTY · Phosphatidylethanolamine · ligand · chains R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.82 | 0.86 | 57 | empty |
| 2 | 880 | 0.77 | 0.80 | 61 | empty |
| 3 | 968 | 0.75 | 0.78 | 77 | empty |
| 4 | 223 | 0.67 | 0.84 | 31 | empty |
| 5 | 300 | 0.64 | 0.81 | 42 | empty |
Interfaces
10 interfaces between chains.
- B–G · 2183 Ų buried · 22 hydrogen bonds · protein-protein
- P–R · 2142 Ų buried · 21 hydrogen bonds · protein-protein
- E–R · 1782 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1585 Ų buried · 29 hydrogen bonds · protein-protein
- A–R · 1191 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7TYF · Human AMYLIN1 receptor in complex with gs and rat amylin peptide · 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 1.00
- 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 0.94
- P30988 · AlphaFold monomer V2.0 prediction for calcitonin receptor (P30988) · a predicted model of the same protein · chain R against A, TM-score 0.85
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.84
- O60894 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 1 (O60894) · a predicted model of the same protein · chain E 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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt O60894
- Every structure of UniProt P59768
- Every structure of UniProt P12969
- Every structure of UniProt P30988
- Elsewhere: RCSB PDB 7TYF · PDBe 7TYF · UniProt P63092 · UniProt P62873 · UniProt O60894 · UniProt P59768 · UniProt P12969 · UniProt P30988
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