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Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron
Analyse Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LXB
- Type
- protein
- Length
- 2,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.34
- Source
- Aplysia californica
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- 7A9, NAG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.34 · 1 distinct chain · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Soluble acetylcholine receptor | protein | 205 | 8% helix, 51% strand | Q8WSF8 |
Ligands and binding sites
- 7A9 · palonosetron · ligand · 7 copies · chains B, C, D, E, A, G, H, I, F, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, D, E, F, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.78 | 0.83 | 53 | 7A9 |
| 2 | 634 | 0.76 | 0.82 | 68 | 7A9 |
| 3 | 513 | 0.66 | 0.77 | 45 | empty |
| 4 | 456 | 0.66 | 0.78 | 47 | 7A9 |
| 5 | 257 | 0.65 | 0.82 | 30 | 7A9 |
Interfaces
14 interfaces between chains.
- H–I · 1352 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1352 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1350 Ų buried · 11 hydrogen bonds · protein-protein
- F–J · 1337 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1305 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 5LXB · Crystal structure of a mutant binding protein (5HTBP-achbp) in complex with palonosetron · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8WSF8
- Elsewhere: RCSB PDB 5LXB · PDBe 5LXB · UniProt Q8WSF8
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