Research workbench
Activated turkey BETA1 adrenoceptor with bound partial agonist xamoterol and nanobody NB6B9
Analyse Activated turkey BETA1 adrenoceptor with bound partial agonist xamoterol and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H7N
- Type
- protein
- Length
- 1,031 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1; Beta-1 adrenergic receptor; Camelid antibody fragment NB6B9
- UniProt
- P0AA25, P07700
- Ligands
- 2CV, FVK, NA
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Thioredoxin 1 | protein | 107 | 35% helix, 27% strand | P0AA25 |
| A | Beta-1 adrenergic receptor | protein | 291 | 81% helix, 0% strand | P07700 |
| F | Thioredoxin 1 | protein | 107 | 36% helix, 25% strand | P0AA25 |
| B | Beta-1 adrenergic receptor | protein | 285 | 83% helix, 0% strand | P07700 |
| C | Camelid antibody fragment NB6B9 | protein | 120 | 5% helix, 54% strand | — |
| D | Camelid antibody fragment NB6B9 | protein | 121 | 5% helix, 54% strand | — |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 5 copies · chains A, B
- FVK · ~{N}-[2-[[(2~{S})-2-oxidanyl-3-(4-oxidanylphenoxy) propyl]amino]ethyl]morpholine-4-carboxamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.77 | 0.79 | 80 | 2CV |
| 2 | 308 | 0.74 | 0.86 | 43 | FVK |
| 3 | 325 | 0.73 | 0.85 | 43 | FVK |
| 4 | 314 | 0.59 | 0.77 | 37 | empty |
| 5 | 279 | 0.59 | 0.78 | 30 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1239 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1206 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 225 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 153 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6H7N · ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST XAMOTEROL AND NANOBODY… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · a predicted model of the same protein · chain F against A, TM-score 0.97
- 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 0.91
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 P0AA25
- Every structure of UniProt P07700
- Elsewhere: RCSB PDB 6H7N · PDBe 6H7N · UniProt P0AA25 · UniProt P07700
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