Research workbench
X-ray structure of acetylcholine binding protein (achbp) complexed with a small molecule
Analyse X-ray structure of acetylcholine binding protein (achbp) complexed with a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2Q
- Type
- protein
- Length
- 999 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 8L3
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Acetylcholine-binding protein | protein | 203 | 8% helix, 48% strand | P58154 |
| A | Acetylcholine-binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 198 | 9% helix, 48% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 200 | 9% helix, 49% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 200 | 9% helix, 48% strand | P58154 |
Ligands and binding sites
- 8L3 · 3-[[4-[(3,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]pyridine · ligand · 5 copies · chains D, A, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.74 | 0.84 | 46 | 8L3 |
| 2 | 427 | 0.73 | 0.83 | 49 | 8L3 |
| 3 | 599 | 0.73 | 0.80 | 75 | empty |
| 4 | 256 | 0.70 | 0.85 | 33 | 8L3 |
| 5 | 233 | 0.70 | 0.86 | 26 | 8L3 |
Interfaces
5 interfaces between chains.
- C–E · 1330 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1319 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1317 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1313 Ų buried · 16 hydrogen bonds · protein-protein
- D–A · 1272 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5Y2Q · X-ray structure of acetylcholine binding protein (AChBP) complexed with a small molecule · the same entry in another collection · chain E against E, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P58154
- Elsewhere: RCSB PDB 5Y2Q · PDBe 5Y2Q · UniProt P58154
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