MolNFT v1 · #183063 · protein
X-ray structure of acetylcholine-binding protein (achbp) in complex with FL001856.
7NDP: “X-ray structure of acetylcholine-binding protein (achbp) in complex with FL001856.”. X-ray diffraction, 4 ligands (U8T, NAG, CL), 20 pockets (best druggability 0.84). MolNFT v1 #183063 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NDP
- Type
- protein
- Length
- 2,019 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- U8T, NAG, CL, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acetylcholine-binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 202 | 8% helix, 49% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 200 | 9% helix, 49% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 203 | 8% helix, 48% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 206 | 8% helix, 48% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 205 | 8% helix, 48% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 202 | 8% helix, 49% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 198 | 9% helix, 49% strand | P58154 |
Ligands and binding sites
- U8T · 6-bromanylspiro[3~{H}-chromene-2,4'-piperidine]-4-one · ligand · 8 copies · chains B, C, D, E, A, G, H, I, J, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains D, F, A, I, B, H, C, G, E, J
- CL · Chloride ion · ion · 2 copies · chains H, I, J
- SO4 · Sulfate ion · ion · chains G, H
- GOL · Glycerol · additive · 5 copies · chains A, B, E, D
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 | 806 | 0.84 | 0.87 | 108 | empty |
| 2 | 1110 | 0.84 | 0.85 | 120 | empty |
| 3 | 294 | 0.76 | 0.88 | 39 | empty |
| 4 | 451 | 0.74 | 0.83 | 41 | empty |
| 5 | 293 | 0.74 | 0.86 | 27 | empty |
Interfaces
21 interfaces between chains.
- G–H · 1367 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1363 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1348 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1344 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1341 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7NDP · X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001856. · the same entry in another collection · chain B against B, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain I 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 7NDP · PDBe 7NDP · UniProt P58154
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