Research workbench
X-ray structure of acetylcholine-binding protein (achbp) in complex with FL001888.
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
- 7NDV
- Type
- protein
- Length
- 2,041 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- U8Q, NAG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 202 | 8% helix, 49% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 205 | 8% helix, 48% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| D, I | Acetylcholine-binding protein | protein | 203 | 8% helix, 48% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 200 | 9% helix, 49% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 204 | 8% helix, 46% strand | P58154 |
| G | Acetylcholine-binding protein | protein | 210 | 8% helix, 46% strand | P58154 |
| H | Acetylcholine-binding protein | protein | 212 | 8% helix, 46% strand | P58154 |
| J | Acetylcholine-binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
Ligands and binding sites
- U8Q · 4-[4-(trifluoromethyl)phenoxy]piperidine · ligand · 9 copies · chains A, B, C, D, E, F, G, J, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, I, B, H, C, G, D, F
- SO4 · Sulfate ion · ion · 4 copies · chains D, E, G, H, I, F, 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 | 1029 | 0.84 | 0.85 | 124 | empty |
| 2 | 1165 | 0.84 | 0.85 | 122 | empty |
| 3 | 785 | 0.80 | 0.84 | 63 | empty |
| 4 | 261 | 0.75 | 0.88 | 25 | U8Q |
| 5 | 344 | 0.73 | 0.85 | 52 | U8Q |
Interfaces
21 interfaces between chains.
- F–G · 1482 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1454 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1435 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1420 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1418 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7NDV · X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001888. · the same entry in another collection · chain H against H, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain C 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 7NDV · PDBe 7NDV · UniProt P58154
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