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Cryo-EM structure of SHU9119-bound melanocortin-1 receptor in complex with gs protein and NB35
Analyse Cryo-EM structure of SHU9119-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
- 7F4I
- 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
- 8 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 39% 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 | 55 | 53% helix, 0% strand | P59768 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 234 | 49% 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, 47% strand | P62873 |
| R | Melanocortin-1 receptor | protein | 266 | 83% helix, 0% strand | — |
| U | SHU9119 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains R, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.83 | 0.86 | 77 | empty |
| 2 | 1116 | 0.77 | 0.79 | 69 | empty |
| 3 | 650 | 0.74 | 0.80 | 74 | empty |
| 4 | 690 | 0.71 | 0.78 | 54 | empty |
| 5 | 52 | 0.49 | 0.86 | 14 | empty |
Interfaces
7 interfaces between chains.
- G–B · 2251 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1507 Ų buried · 22 hydrogen bonds · protein-protein
- A–R · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- R–U · 858 Ų buried · 6 hydrogen bonds · protein-protein
- A–N · 781 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (nonstandard, disulfide).
Compared structures
- 7F4I · Cryo-EM structure of SHU9119-bound melanocortin-1 receptor in complex with Gs protein and… · the same entry in another collection · chain U against U, 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 7F4I · PDBe 7F4I · UniProt P59768 · UniProt P62873
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