Research workbench
Active melanocortin-4 receptor (MC4R)- gs protein complex bound to agonist ndp-alpha-msh at 2.86 a resolution.
Analyse Active melanocortin-4 receptor (MC4R)- gs protein complex bound to agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PIV
- Type
- protein
- Length
- 977 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanocortin receptor 4; Ndp-alpha-msh (other names afamelanotide; Isoform gnas-2 of…
- UniProt
- P32245, P63092, P54311, P63213
- Ligands
- CA
- Pockets
- 11 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Melanocortin receptor 4 | protein | 260 | 83% helix, 0% strand | P32245 |
| P | Ndp-alpha-msh (other names afamelanotide | protein | 13 | 0% helix, 0% strand | — |
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 183 | 48% helix, 20% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 47% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 51% helix, 0% strand | P63213 |
| N | Camelid antibody vhh fragment - nanobody 35 | protein | 128 | 5% helix, 43% 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.81 | 0.85 | 55 | empty |
| 2 | 982 | 0.77 | 0.79 | 66 | empty |
| 3 | 800 | 0.73 | 0.79 | 53 | empty |
| 4 | 165 | 0.67 | 0.87 | 24 | empty |
| 5 | 233 | 0.63 | 0.82 | 35 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2218 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1540 Ų buried · 22 hydrogen bonds · protein-protein
- R–A · 1372 Ų buried · 10 hydrogen bonds · protein-protein
- R–P · 929 Ų buried · 7 hydrogen bonds · protein-protein
- A–N · 927 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).
Compared structures
- 7PIV · Active Melanocortin-4 receptor (MC4R)- Gs protein complex bound to agonist NDP-alpha-MSH… · 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 0.96
- P63213 · 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 0.91
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 P63213
- Elsewhere: RCSB PDB 7PIV · PDBe 7PIV · UniProt P32245 · UniProt P63092 · UniProt P54311 · UniProt P63213
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