Research workbench
Turkey BETA1 adrenergic receptor with stabilising mutations and bound antagonist cyanopindolol
Analyse Turkey BETA1 adrenergic receptor with stabilising mutations and bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YCY
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1 adrenergic receptor
- UniProt
- P07700
- Ligands
- SOG, P32, NA
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1 adrenergic receptor | protein | 288 | 81% helix, 0% strand | P07700 |
| B | Beta-1 adrenergic receptor | protein | 291 | 81% helix, 0% strand | P07700 |
Ligands and binding sites
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 5 copies · chains A, B
- P32 · 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.82 | 0.82 | 68 | SOG |
| 2 | 500 | 0.76 | 0.83 | 49 | P32 |
| 3 | 472 | 0.75 | 0.83 | 47 | P32 |
| 4 | 306 | 0.62 | 0.79 | 29 | empty |
| 5 | 291 | 0.60 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2YCY · Turkey BETA1 adrenergic receptor with stabilising mutations and bound antagonist… · 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 B 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 2YCY · PDBe 2YCY · UniProt P07700
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