Research workbench
X-ray structure of acetylcholine binding protein (achbp) in complex with 4-(4-methylpiperidin-1-yl)-6-(4-(TRIFLUOROMETHYL)PHENYL) pyrimidin-2-amine
Analyse X-ray structure of acetylcholine binding protein (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
- 4QAC
- Type
- protein
- Length
- 2,091 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- KK3, NAG, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Acetylcholine-binding protein | protein | 209 | 11% helix, 47% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 205 | 10% helix, 47% strand | P58154 |
| C, I | Acetylcholine-binding protein | protein | 208 | 11% helix, 46% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 213 | 12% helix, 46% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 211 | 9% helix, 45% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 213 | 11% helix, 46% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 210 | 11% helix, 47% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 205 | 10% helix, 47% strand | P58154 |
Ligands and binding sites
- KK3 · 4-(4-methylpiperidin-1-yl)-6-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine · 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, F, B, J, D, H, E, G, C, I
- PO4 · Phosphate ion · ion · 10 copies · chains A, E, B, C, D, F, J, G, H, I
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 | 929 | 0.79 | 0.81 | 99 | KK3 |
| 2 | 741 | 0.77 | 0.82 | 79 | empty |
| 3 | 400 | 0.74 | 0.84 | 50 | KK3 |
| 4 | 448 | 0.74 | 0.83 | 52 | KK3 |
| 5 | 467 | 0.74 | 0.83 | 63 | KK3 |
Interfaces
20 interfaces between chains.
- F–J · 1616 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1608 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1608 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1598 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1592 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4QAC · X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH… · the same entry in another collection · chain D against D, 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 0.97
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 4QAC · PDBe 4QAC · UniProt P58154
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