MolNFT v1 · #114424 · protein
X-ray crystal structure of lymnaea stagnalis acetylcholine binding protein (ls-achbp) in complex with 5-fluoronicotine (ti-4650)
5BP0 · Acetylcholine-binding protein: “X-ray crystal structure of lymnaea stagnalis acetylcholine binding protein (ls-achbp) in complex with…”. X-ray diffraction, 3 ligands (FN1, NAG, PO4), 20 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5BP0
- Type
- protein
- Length
- 2,022 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- FN1, NAG, PO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 10 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 199 | 10% helix, 49% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 205 | 10% helix, 47% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 208 | 11% helix, 46% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 207 | 10% helix, 46% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 202 | 10% helix, 47% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 193 | 10% helix, 49% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 201 | 10% helix, 47% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 201 | 10% helix, 49% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 203 | 10% helix, 47% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 203 | 9% helix, 47% strand | P58154 |
Ligands and binding sites
- FN1 · 5-fluoronicotine · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 10 copies · chains A, E, B, C, D, F, G, H, 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 | 77 | 0.73 | 0.96 | 17 | FN1 |
| 2 | 250 | 0.72 | 0.86 | 26 | FN1 |
| 3 | 712 | 0.69 | 0.77 | 76 | empty |
| 4 | 170 | 0.69 | 0.87 | 29 | FN1 |
| 5 | 151 | 0.68 | 0.88 | 26 | FN1 |
Interfaces
19 interfaces between chains.
- H–I · 1545 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1501 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1465 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1461 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1431 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5BP0 · PDBe 5BP0 · UniProt P58154
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