Research workbench
Structure of BETA2 adrenoceptor bound to carazolol and inactive-state stabilizing nanobody, NB60
Analyse Structure of BETA2 adrenoceptor bound to carazolol and inactive-state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQH
- Type
- protein
- Length
- 1,030 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,BETA-2 adrenergic receptor; NANOBODY60, NB60
- EC
- 3.2.1.17
- UniProt
- P00720, P07550
- Ligands
- CAU, CLR
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,BETA-2 adrenergic receptor (EC 3.2.1.17) | protein | 391 | 80% helix, 0% strand | P00720, P07550 |
| B | ENDOLYSIN,BETA-2 adrenergic receptor (EC 3.2.1.17) | protein | 402 | 77% helix, 0% strand | P00720, P07550 |
| D | NANOBODY60, NB60 | protein | 117 | 3% helix, 56% strand | — |
| C | NANOBODY60, NB60 | protein | 120 | 3% helix, 58% strand | — |
Ligands and binding sites
- CAU · (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.79 | 0.87 | 38 | CAU |
| 2 | 540 | 0.76 | 0.83 | 54 | CAU |
| 3 | 103 | 0.61 | 0.87 | 24 | empty |
| 4 | 355 | 0.56 | 0.74 | 50 | empty |
| 5 | 136 | 0.53 | 0.81 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 851 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 805 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 707 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5JQH · Structure of beta2 adrenoceptor bound to carazolol and inactive-state stabilizing… · the same entry in another collection · chain A against A, TM-score 1.00
- P07550 · AlphaFold monomer V2.0 prediction for beta-2 adrenergic receptor (P07550) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P00720
- Every structure of UniProt P07550
- Elsewhere: RCSB PDB 5JQH · PDBe 5JQH · UniProt P00720 · UniProt P07550
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