Research workbench
Cryo-EM structure of neuropeptide Y Y2 receptor in complex with npy and gi
Analyse Cryo-EM structure of neuropeptide Y Y2 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
- 7X9B
- Type
- protein
- Length
- 946 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P49146, P01303
- Pockets
- 11 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 44% helix, 14% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 6% helix, 37% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 52% helix, 0% strand | P59768 |
| R | Neuropeptide Y receptor type 2 | protein | 302 | 71% helix, 1% strand | P49146 |
| P | Neuropeptide Y | protein | 36 | 50% helix, 0% strand | P01303 |
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 | 576 | 0.81 | 0.86 | 60 | empty |
| 2 | 1159 | 0.71 | 0.75 | 82 | empty |
| 3 | 260 | 0.66 | 0.83 | 35 | empty |
| 4 | 157 | 0.60 | 0.83 | 33 | empty |
| 5 | 123 | 0.56 | 0.83 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2112 Ų buried · 12 hydrogen bonds · protein-protein
- R–P · 1387 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1296 Ų buried · 7 hydrogen bonds · protein-protein
- A–R · 1204 Ų buried · 12 hydrogen bonds · protein-protein
- B–R · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 7X9B · Cryo-EM structure of neuropeptide Y Y2 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
- P49146 · AlphaFold monomer V2.0 prediction for neuropeptide Y receptor type 2 (P49146) · a predicted model of the same protein · chain R against A, TM-score 0.91
- 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 0.88
- 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 P against A, TM-score 0.68
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P49146
- Every structure of UniProt P01303
- Elsewhere: RCSB PDB 7X9B · PDBe 7X9B · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P49146 · UniProt P01303
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