MolNFT v1 · #152239 · protein
Activated turkey BETA1 adrenoceptor with bound agonist formoterol and nanobody NB80
6IBL · Thioredoxin 1,BETA-1 adrenergic receptor: “Activated turkey BETA1 adrenoceptor with bound agonist formoterol and nanobody NB80”. X-ray diffraction, 3 ligands (2CV, H98, NA), 13 pockets (best druggability 0.80). MolNFT v1 #152239 on…
- PDB
- 6IBL
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1,BETA-1 adrenergic receptor; Camelid antibody fragment NB80
- UniProt
- P0AA25, P07700
- Ligands
- 2CV, H98, NA
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin 1,BETA-1 adrenergic receptor | protein | 397 | 69% helix, 6% strand | P0AA25, P07700 |
| C | Camelid antibody fragment NB80 | protein | 119 | 5% helix, 55% strand | — |
| B | Thioredoxin 1,BETA-1 adrenergic receptor | protein | 391 | 69% helix, 7% strand | P0AA25, P07700 |
| D | Camelid antibody fragment NB80 | protein | 120 | 5% helix, 53% strand | — |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 8 copies · chains A, B
- H98 · ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.80 | 0.84 | 79 | H98, 2CV |
| 2 | 360 | 0.72 | 0.83 | 43 | H98 |
| 3 | 374 | 0.68 | 0.81 | 39 | 2CV |
| 4 | 310 | 0.61 | 0.78 | 40 | empty |
| 5 | 283 | 0.60 | 0.79 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1240 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1196 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6IBL · ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND AGONIST FORMOTEROL AND NANOBODY Nb80 · 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 0.70
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 6IBL · PDBe 6IBL · UniProt P0AA25 · UniProt P07700
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