Research workbench
Neuropeptide Y Y1 receptor (NPY1R) in complex with G protein and its endogeneous peptide-agonist neuropeptide Y (npy)
Analyse Neuropeptide Y Y1 receptor (NPY1R) in complex with G protein and its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGX
- Type
- protein
- Length
- 1,149 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropeptide Y receptor type 1; Neuropeptide Y; Guanine nucleotide-binding protein G(I)…
- UniProt
- P25929, P01303, P63096, P62873, P59768
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Neuropeptide Y receptor type 1 | protein | 280 | 75% helix, 0% strand | P25929 |
| L | Neuropeptide Y | protein | 22 | 50% helix, 0% strand | P01303 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 224 | 45% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 45% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 52% helix, 0% strand | P59768 |
| S | Single-chain antibody fv fragment (SCFV16) | protein | 231 | 3% helix, 48% strand | — |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.82 | 0.83 | 68 | empty |
| 2 | 89 | 0.75 | 0.97 | 20 | empty |
| 3 | 80 | 0.74 | 0.97 | 16 | empty |
| 4 | 73 | 0.71 | 0.96 | 23 | empty |
| 5 | 229 | 0.66 | 0.84 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2105 Ų buried · 10 hydrogen bonds · protein-protein
- R–L · 1319 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 13 hydrogen bonds · protein-protein
- R–A · 964 Ų buried · 7 hydrogen bonds · protein-protein
- A–S · 537 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 7VGX · Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and its endogeneous… · the same entry in another collection · chain S against S, 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
- 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 0.92
- 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 0.84
- 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 0.81
- P01303 · AlphaFold monomer V2.0 prediction for pro-neuropeptide Y (P01303) · a predicted model of the same protein · chain L against A, TM-score 0.55
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 P01303
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7VGX · PDBe 7VGX · UniProt P25929 · UniProt P01303 · UniProt P63096 · UniProt P62873 · UniProt P59768
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