Research workbench
Cryo-EM structure of afamelanotide-bound melanocortin-1 receptor in complex with gs protein and SCFV16
Analyse Cryo-EM structure of afamelanotide-bound melanocortin-1 receptor in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F4F
- Type
- protein
- Length
- 1,139 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCFV16; Melanocortin-1 receptor; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P59768, P62873
- Ligands
- CA
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | SCFV16 | protein | 230 | 5% helix, 45% strand | — |
| R | Melanocortin-1 receptor | protein | 269 | 86% helix, 0% strand | — |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 232 | 50% helix, 16% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 55% helix, 0% strand | P59768 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 8% helix, 45% strand | P62873 |
| F | Afamelanotide | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains R, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.82 | 0.87 | 57 | empty |
| 2 | 1112 | 0.78 | 0.80 | 74 | empty |
| 3 | 210 | 0.55 | 0.79 | 37 | empty |
| 4 | 182 | 0.51 | 0.77 | 19 | empty |
| 5 | 166 | 0.50 | 0.78 | 28 | empty |
Interfaces
7 interfaces between chains.
- G–B · 2232 Ų buried · 13 hydrogen bonds · protein-protein
- R–A · 1503 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1495 Ų buried · 30 hydrogen bonds · protein-protein
- R–F · 934 Ų buried · 11 hydrogen bonds · protein-protein
- S–A · 618 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).
Compared structures
- 7F4F · Cryo-EM structure of afamelanotide-bound melanocortin-1 receptor in complex with Gs… · the same entry in another collection · chain F against F, 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 0.98
- 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
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 P59768
- Every structure of UniProt P62873
- Elsewhere: RCSB PDB 7F4F · PDBe 7F4F · UniProt P59768 · UniProt P62873
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