Research workbench
Turkey BETA1 adrenergic receptor with stabilising mutations and bound partial agonist dobutamine (crystal DOB102)
Analyse Turkey BETA1 adrenergic receptor with stabilising mutations and bound partial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y01
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1 adrenergic receptor
- UniProt
- P07700
- Ligands
- 2CV, Y01, Y00
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1 adrenergic receptor | protein | 286 | 84% helix, 0% strand | P07700 |
| B | Beta-1 adrenergic receptor | protein | 298 | 82% helix, 0% strand | P07700 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 10 copies · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A, B
- Y00 · Dobutamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.83 | 0.83 | 74 | Y01, 2CV |
| 2 | 504 | 0.73 | 0.82 | 40 | Y00 |
| 3 | 361 | 0.71 | 0.83 | 41 | Y00 |
| 4 | 373 | 0.65 | 0.79 | 26 | empty |
| 5 | 331 | 0.63 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2Y01 · Turkey BETA1 adrenergic receptor with stabilising mutations and bound partial agonist… · the same entry in another collection · chain A against A, TM-score 1.00
- P07700 · AlphaFold monomer V2.0 prediction for beta-1 adrenergic receptor (P07700) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07700
- Elsewhere: RCSB PDB 2Y01 · PDBe 2Y01 · UniProt P07700
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