MolNFT v1 · #104435 · protein
X-ray structure of acetylcholine binding protein (achbp) in complex with 6-(4-methoxyphenyl)-N4-octylpyrimidine-2,4-diamine
4QAA · Acetylcholine-binding protein: “X-ray structure of acetylcholine binding protein (achbp) in complex with…”. X-ray diffraction, 3 ligands (KK1, NAG, PO4), 20 pockets (best druggability 0.75). MolNFT v1 #104435 on GenesisL1: 3D…
- PDB
- 4QAA
- Type
- protein
- Length
- 2,078 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- KK1, NAG, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 207 | 10% helix, 44% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 207 | 10% helix, 47% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 209 | 11% helix, 45% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 213 | 11% helix, 45% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 205 | 11% helix, 47% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 209 | 11% helix, 45% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 208 | 11% helix, 46% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 207 | 11% helix, 45% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 207 | 11% helix, 44% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 206 | 10% helix, 46% strand | P58154 |
Ligands and binding sites
- KK1 · 6-(4-methoxyphenyl)-N~4~-octylpyrimidine-2,4-diamine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, I, B, H, C, G, D, F, E, J
- PO4 · Phosphate ion · ion · 19 copies · chains A, B, E, H, C, D, F, J, G, 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 | 392 | 0.75 | 0.85 | 48 | KK1 |
| 2 | 398 | 0.72 | 0.83 | 46 | KK1 |
| 3 | 452 | 0.72 | 0.82 | 40 | KK1 |
| 4 | 439 | 0.71 | 0.82 | 39 | KK1 |
| 5 | 715 | 0.71 | 0.78 | 64 | PO4 |
Interfaces
20 interfaces between chains.
- D–E · 1751 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1631 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 1596 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1576 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1511 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4QAA · X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IN COMPLEX WITH… · the same entry in another collection · chain J against J, 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 0.95
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 4QAA · PDBe 4QAA · UniProt P58154
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