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Cryo-EM structure of alpha-msh-bound melanocortin-1 receptor in complex with gs protein and NB35
Analyse Cryo-EM structure of alpha-msh-bound melanocortin-1 receptor in complex with gs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F4D
- Type
- protein
- Length
- 1,030 residues
- Chains
- 6
- 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
- 12 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P59768 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 234 | 52% helix, 18% strand | — |
| N | Nanobody 35 | protein | 127 | 5% helix, 45% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 46% strand | P62873 |
| R | Melanocortin-1 receptor | protein | 263 | 86% helix, 0% strand | — |
| M | Alpha-melanocyte-stimulating hormone | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains R, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.82 | 0.88 | 56 | empty |
| 2 | 1067 | 0.79 | 0.80 | 69 | empty |
| 3 | 711 | 0.73 | 0.79 | 63 | empty |
| 4 | 337 | 0.67 | 0.82 | 52 | empty |
| 5 | 191 | 0.65 | 0.85 | 29 | empty |
Interfaces
7 interfaces between chains.
- G–B · 2187 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1552 Ų buried · 29 hydrogen bonds · protein-protein
- A–R · 1439 Ų buried · 15 hydrogen bonds · protein-protein
- R–M · 1001 Ų buried · 15 hydrogen bonds · protein-protein
- A–N · 851 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7F4D · Cryo-EM structure of alpha-MSH-bound melanocortin-1 receptor in complex with Gs protein… · the same entry in another collection · chain M against M, 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 0.99
- 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 7F4D · PDBe 7F4D · UniProt P59768 · UniProt P62873
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