Research workbench
Cryo-EM structure of neuropeptide Y Y4 receptor in complex with pp and gi
Analyse Cryo-EM structure of neuropeptide Y Y4 receptor in complex with pp and gi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X9C
- Type
- protein
- Length
- 945 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropeptide Y receptor type 4; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P50391, P63096, P62873, P59768, P01298
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Neuropeptide Y receptor type 4 | protein | 302 | 73% helix, 1% strand | P50391 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 44% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 9% helix, 44% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 52% helix, 0% strand | P59768 |
| P | Pancreatic hormone | protein | 36 | 50% helix, 0% strand | P01298 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.82 | 0.87 | 64 | empty |
| 2 | 196 | 0.72 | 0.89 | 34 | empty |
| 3 | 677 | 0.67 | 0.76 | 64 | empty |
| 4 | 153 | 0.57 | 0.82 | 30 | empty |
| 5 | 176 | 0.52 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1983 Ų buried · 13 hydrogen bonds · protein-protein
- R–P · 1443 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1207 Ų buried · 18 hydrogen bonds · protein-protein
- R–A · 1091 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 7X9C · Cryo-EM structure of neuropeptide Y Y4 receptor in complex with PP and Gi · the same entry in another collection · chain P against P, 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 C against A, TM-score 0.90
- P50391 · AlphaFold monomer V2.0 prediction for neuropeptide Y receptor type 4 (P50391) · a predicted model of the same protein · chain R against A, TM-score 0.89
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82
- P01298 · AlphaFold monomer V2.0 prediction for pancreatic prohormone (P01298) · a predicted model of the same protein · chain P against A, TM-score 0.71
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 P50391
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P01298
- Elsewhere: RCSB PDB 7X9C · PDBe 7X9C · UniProt P50391 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P01298
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