Research workbench
The crystal structure of human neuropeptide Y Y1 receptor with ur- MK299
Analyse The crystal structure of human neuropeptide Y Y1 receptor with ur- MK299 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZBQ
- Type
- protein
- Length
- 463 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropeptide Y receptor type 1,T4 lysozyme
- EC
- 3.2.1.17
- UniProt
- P25929, A0A097J792
- Ligands
- 9AO
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropeptide Y receptor type 1,T4 lysozyme (EC 3.2.1.17) | protein | 463 | 70% helix, 6% strand | P25929, A0A097J792 |
Ligands and binding sites
- 9AO · N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino) ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.87 | 0.90 | 59 | 9AO |
| 2 | 84 | 0.63 | 0.89 | 18 | empty |
| 3 | 179 | 0.44 | 0.74 | 36 | empty |
| 4 | 186 | 0.43 | 0.73 | 22 | empty |
| 5 | 73 | 0.39 | 0.78 | 12 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZBQ · The Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299 · the same entry in another collection · chain A against A, TM-score 1.00
- P25929 · AlphaFold monomer V2.0 prediction for neuropeptide Y receptor type 1 (P25929) · a predicted model of the same protein · chain A against A, TM-score 0.59
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 A0A097J792
- Elsewhere: RCSB PDB 5ZBQ · PDBe 5ZBQ · UniProt P25929 · UniProt A0A097J792
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