MolNFT v1 · #188579 · protein
Human AMYLIN2 receptor in complex with gs and rat amylin peptide
7TYX · Receptor activity-modifying protein 2: “Human AMYLIN2 receptor in complex with gs and rat amylin peptide”. Electron microscopy, 4 ligands (PLM, Y01, NAG), 15 pockets (best druggability 0.82). MolNFT v1 #188579 on GenesisL1: 3D…
- PDB
- 7TYX
- Type
- protein
- Length
- 1,269 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor activity-modifying protein 2; Amylin peptide; Calcitonin receptor; Guanine…
- UniProt
- O60895, P12969, P30988, P63092, P62873, P59768
- Ligands
- PLM, Y01, NAG, NH2
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Receptor activity-modifying protein 2 | protein | 112 | 69% helix, 1% strand | O60895 |
| P | Amylin peptide | protein | 37 | 32% helix, 0% strand | P12969 |
| R | Calcitonin receptor | protein | 365 | 68% helix, 7% strand | P30988 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 233 | 48% helix, 18% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 53% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 45% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 8 copies · chains P, R
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains R
- NH2 · Amino group · ion · chains P, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.82 | 0.85 | 58 | empty |
| 2 | 928 | 0.76 | 0.79 | 68 | empty |
| 3 | 875 | 0.75 | 0.79 | 77 | empty |
| 4 | 992 | 0.74 | 0.77 | 92 | empty |
| 5 | 299 | 0.68 | 0.83 | 40 | empty |
Interfaces
10 interfaces between chains.
- B–G · 2218 Ų buried · 15 hydrogen bonds · protein-protein
- P–R · 2010 Ų buried · 13 hydrogen bonds · protein-protein
- E–R · 1947 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1532 Ų buried · 30 hydrogen bonds · protein-protein
- R–A · 1133 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7TYX · Human Amylin2 Receptor in complex with Gs and rat amylin peptide · the same entry in another collection · chain N against N, 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
- O60895 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 2 (O60895) · a predicted model of the same protein · chain E against A, TM-score 0.80
- P12969 · AlphaFold monomer V2.0 prediction for islet amyloid polypeptide (P12969) · a predicted model of the same protein · chain P against A, TM-score 0.36
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 O60895
- Every structure of UniProt P12969
- Every structure of UniProt P30988
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7TYX · PDBe 7TYX · UniProt O60895 · UniProt P12969 · UniProt P30988 · UniProt P63092 · UniProt P62873 · UniProt P59768
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