Research workbench
ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST SALBUTAMOL AND NANOBODY Nb6B9
Analyse ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST SALBUTAMOL AND… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H7M
- Type
- protein
- Length
- 1,030 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.76
- Source
- Escherichia coli (strain K12); Lama glama; Meleagris gallopavo
- Molecule
- Thioredoxin 1; Beta-1 adrenergic receptor; Camelid antibody fragment Nb6B9
- UniProt
- P0AA25, P07700
- Ligands
- 2CV, 68H, NA
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.76 · 5 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Thioredoxin 1 | protein | 107 | 35% helix, 25% strand | P0AA25 |
| A | Beta-1 adrenergic receptor | protein | 291 | 81% helix, 1% strand | P07700 |
| C, D | Camelid antibody fragment Nb6B9 | protein | 120 | 3% helix, 56% strand | — |
| F | Thioredoxin 1 | protein | 107 | 35% helix, 25% strand | P0AA25 |
| B | Beta-1 adrenergic receptor | protein | 285 | 82% helix, 1% strand | P07700 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 7 copies · chains A, B
- 68H · Salbutamol · 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.77 | 0.79 | 82 | 2CV |
| 2 | 307 | 0.74 | 0.86 | 41 | 68H |
| 3 | 337 | 0.73 | 0.85 | 45 | 68H |
| 4 | 307 | 0.61 | 0.78 | 38 | empty |
| 5 | 308 | 0.59 | 0.78 | 36 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1206 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1202 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 616 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 206 Ų buried · 1 hydrogen bond · protein-protein
- A–F · 136 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6H7M · Activated turkey BETA1 adrenoceptor with bound partial agonist salbutamol and nanobody… · the same entry in another collection · chain F against F, 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 0.90
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 6H7M · PDBe 6H7M · UniProt P0AA25 · UniProt P07700
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