Research workbench
Cryo-EM structure of neuropeptide Y Y1 receptor in complex with npy and gi
Analyse Cryo-EM structure of neuropeptide Y Y1 receptor in complex with npy and gi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X9A
- Type
- protein
- Length
- 950 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropeptide Y receptor type 1; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P25929, P63096, P62873, P01303
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Neuropeptide Y receptor type 1 | protein | 309 | 71% helix, 2% strand | P25929 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 215 | 42% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 5% helix, 43% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 48% helix, 0% strand | — |
| P | Neuropeptide Y | protein | 36 | 50% helix, 0% strand | P01303 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.82 | 0.86 | 64 | empty |
| 2 | 1086 | 0.72 | 0.76 | 84 | empty |
| 3 | 52 | 0.71 | 0.99 | 20 | empty |
| 4 | 313 | 0.65 | 0.81 | 48 | empty |
| 5 | 56 | 0.50 | 0.86 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1909 Ų buried · 11 hydrogen bonds · protein-protein
- R–P · 1631 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1177 Ų buried · 9 hydrogen bonds · protein-protein
- R–A · 1113 Ų buried · 8 hydrogen bonds · protein-protein
- R–B · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 7X9A · Cryo-EM structure of neuropeptide Y Y1 receptor in complex with NPY 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 0.98
- P25929 · AlphaFold monomer V2.0 prediction for neuropeptide Y receptor type 1 (P25929) · a predicted model of the same protein · chain R against A, TM-score 0.90
- 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 0.83
- P01303 · AlphaFold monomer V2.0 prediction for pro-neuropeptide Y (P01303) · a predicted model of the same protein · chain P against A, TM-score 0.76
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 P25929
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P01303
- Elsewhere: RCSB PDB 7X9A · PDBe 7X9A · UniProt P25929 · UniProt P63096 · UniProt P62873 · UniProt P01303
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