Research workbench
Crystal structure of a mutant binding protein (5HTBP-achbp) in complex with granisetron
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
- 2YME
- Type
- protein
- Length
- 2,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- CWB, NAG, NA, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Soluble acetylcholine receptor | protein | 205 | 9% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- CWB · 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, F, H, I, J
- NA · Sodium ion · metal · chains I
- PO4 · Phosphate ion · ion · 5 copies · chains A, C, E, G, H
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 | 902 | 0.75 | 0.78 | 72 | CWB |
| 2 | 786 | 0.74 | 0.79 | 76 | CWB, NA |
| 3 | 486 | 0.69 | 0.79 | 56 | CWB |
| 4 | 394 | 0.69 | 0.81 | 48 | CWB |
| 5 | 606 | 0.67 | 0.76 | 69 | CWB |
Interfaces
12 interfaces between chains.
- D–E · 1318 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1315 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1307 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1281 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 2YME · Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with granisetron · the same entry in another collection · chain F against F, 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 2YME · PDBe 2YME · UniProt Q8WSF8
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