Research workbench
Activated turkey BETA1 adrenoceptor with bound weak partial agonist cyanopindolol and nanobody NB6B9
Analyse Activated turkey BETA1 adrenoceptor with bound weak partial agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H7O
- Type
- protein
- Length
- 1,025 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, P32, NA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Thioredoxin 1 | protein | 107 | 36% helix, 26% strand | P0AA25 |
| A | Beta-1 adrenergic receptor | protein | 290 | 82% helix, 0% strand | P07700 |
| C | Camelid antibody fragment NB6B9 | protein | 120 | 5% helix, 55% strand | — |
| B | Beta-1 adrenergic receptor | protein | 280 | 84% helix, 0% strand | P07700 |
| D | Camelid antibody fragment NB6B9 | protein | 121 | 5% helix, 55% strand | — |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 7 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 · 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 | 1111 | 0.77 | 0.78 | 96 | 2CV |
| 2 | 338 | 0.75 | 0.86 | 42 | P32 |
| 3 | 386 | 0.74 | 0.85 | 45 | P32 |
| 4 | 540 | 0.63 | 0.75 | 60 | empty |
| 5 | 299 | 0.59 | 0.78 | 37 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1219 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1143 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 573 Ų buried · 3 hydrogen bonds · protein-protein
- F–B · 177 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 172 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6H7O · ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND WEAK PARTIAL AGONIST CYANOPINDOLOL AND… · 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 E against A, TM-score 0.98
- 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 0.92
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 6H7O · PDBe 6H7O · UniProt P0AA25 · UniProt P07700
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