Research workbench
Structure of BETA2 adrenoceptor bound to hydroxybenzylisoproterenol and an engineered nanobody
Analyse Structure of BETA2 adrenoceptor bound to hydroxybenzylisoproterenol and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LDL
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme, beta-2 adrenergic receptor; Camelid antibody fragment
- EC
- 3.2.1.17
- UniProt
- P00720, P07550
- Ligands
- XQC, 1WV, NA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme, beta-2 adrenergic receptor (EC 3.2.1.17) | protein | 454 | 72% helix, 3% strand | P00720, P07550 |
| B | Camelid antibody fragment | protein | 120 | 3% helix, 56% strand | — |
Ligands and binding sites
- XQC · 4-[(1R)-1-hydroxy-2-{[1-(4-hydroxyphenyl)-2-methylpropan-2-yl]amino}ethyl]benzene-1,2-diol · ligand · chains A
- 1WV · (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.79 | 0.81 | 84 | XQC, 1WV |
| 2 | 369 | 0.65 | 0.79 | 36 | empty |
| 3 | 306 | 0.58 | 0.77 | 36 | empty |
| 4 | 113 | 0.40 | 0.75 | 19 | empty |
| 5 | 54 | 0.35 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1178 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4LDL · Structure of beta2 adrenoceptor bound to hydroxybenzylisoproterenol and an engineered… · 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 0.61
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 4LDL · PDBe 4LDL · UniProt P00720 · UniProt P07550
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