Research workbench
Human AMYLIN3 receptor in complex with gs and rat amylin peptide
Analyse Human AMYLIN3 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
- 7TZF
- Type
- protein
- Length
- 1,272 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor activity-modifying protein 3; Amylin peptide; Calcitonin receptor; Guanine…
- UniProt
- O60896, P12969, P30988, P63092, P62873, P59768
- Ligands
- PLM, Y01, P42, NAG, NH2
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Receptor activity-modifying protein 3 | protein | 114 | 62% helix, 1% strand | O60896 |
| P | Amylin peptide | protein | 37 | 41% helix, 3% strand | P12969 |
| R | Calcitonin receptor | protein | 367 | 67% helix, 7% strand | P30988 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 232 | 49% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 47% 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 | 5% helix, 45% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 11 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, R
- NH2 · Amino group · ion · chains P, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.82 | 0.86 | 56 | empty |
| 2 | 900 | 0.77 | 0.80 | 62 | empty |
| 3 | 856 | 0.73 | 0.78 | 67 | empty |
| 4 | 857 | 0.71 | 0.76 | 74 | empty |
| 5 | 278 | 0.70 | 0.85 | 30 | empty |
Interfaces
9 interfaces between chains.
- B–G · 2218 Ų buried · 23 hydrogen bonds · protein-protein
- P–R · 2085 Ų buried · 20 hydrogen bonds · protein-protein
- E–R · 1994 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1499 Ų buried · 26 hydrogen bonds · protein-protein
- R–A · 1166 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7TZF · Human Amylin3 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 0.93
- P30988 · AlphaFold monomer V2.0 prediction for calcitonin receptor (P30988) · a predicted model of the same protein · chain R against A, TM-score 0.84
- O60896 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 3 (O60896) · a predicted model of the same protein · chain E against A, TM-score 0.75
- 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 O60896
- 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 7TZF · PDBe 7TZF · UniProt O60896 · UniProt P12969 · UniProt P30988 · UniProt P63092 · UniProt P62873 · UniProt P59768
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