Research workbench
Cryo-EM structure of afamelanotide-bound melanocortin-1 receptor in complex with gs protein, NB35 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
- 7F4H
- Type
- protein
- Length
- 1,266 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2; Guanine…
- UniProt
- P59768, P62873
- Ligands
- CA
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 7 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 53% helix, 0% strand | P59768 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 234 | 48% helix, 18% strand | — |
| N | Nanobody 35 | protein | 127 | 5% helix, 43% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 8% helix, 45% strand | P62873 |
| R | Melanocortin-1 receptor | protein | 267 | 87% helix, 0% strand | — |
| S | SCFV16 | protein | 230 | 5% helix, 47% strand | — |
| 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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.80 | 0.86 | 55 | empty |
| 2 | 1104 | 0.78 | 0.80 | 76 | empty |
| 3 | 764 | 0.75 | 0.80 | 66 | empty |
| 4 | 441 | 0.70 | 0.81 | 75 | empty |
| 5 | 167 | 0.67 | 0.87 | 24 | empty |
Interfaces
9 interfaces between chains.
- G–B · 2351 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1589 Ų buried · 34 hydrogen bonds · protein-protein
- A–R · 1358 Ų buried · 14 hydrogen bonds · protein-protein
- R–F · 934 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 850 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).
Compared structures
- 7F4H · Cryo-EM structure of afamelanotide-bound melanocortin-1 receptor in complex with Gs… · the same entry in another collection · chain B against B, 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 0.92
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 7F4H · PDBe 7F4H · UniProt P59768 · UniProt P62873
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