Research workbench
Cryo-EM structure of the agonist setmelanotide bound to the active melanocortin-4 receptor (MC4R) in complex with the heterotrimeric gs protein at 2.6 a resolution.
Analyse Cryo-EM structure of the agonist setmelanotide bound to the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PIU
- Type
- protein
- Length
- 976 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanocortin receptor 4; Setmelanotide (other names rm-493; Isoform gnas-2 of guanine…
- UniProt
- P32245, P63092, P54311, P63212
- Ligands
- CA
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Melanocortin receptor 4 | protein | 259 | 85% helix, 0% strand | P32245 |
| P | Setmelanotide (other names rm-493 | protein | 8 | 0% helix, 0% strand | — |
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 189 | 47% helix, 20% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 48% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 51% helix, 0% strand | P63212 |
| N | Camelid antibody fragment - nanobody 35 | protein | 128 | 5% helix, 44% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains R, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.81 | 0.85 | 57 | empty |
| 2 | 999 | 0.77 | 0.79 | 73 | empty |
| 3 | 770 | 0.73 | 0.79 | 54 | empty |
| 4 | 166 | 0.68 | 0.88 | 24 | empty |
| 5 | 446 | 0.68 | 0.80 | 64 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2288 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 19 hydrogen bonds · protein-protein
- R–A · 1467 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 951 Ų buried · 14 hydrogen bonds · protein-protein
- R–P · 749 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 d-amino (disulfide, D-amino acid).
Compared structures
- 7PIU · Cryo-EM structure of the agonist setmelanotide bound to the active melanocortin-4… · the same entry in another collection · chain N against N, TM-score 1.00
- P54311 · 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
- P32245 · AlphaFold monomer V2.0 prediction for melanocortin receptor 4 (P32245) · a predicted model of the same protein · chain R against A, TM-score 0.95
- 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 0.66
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 P32245
- Every structure of UniProt P63092
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7PIU · PDBe 7PIU · UniProt P32245 · UniProt P63092 · UniProt P54311 · UniProt P63212
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