MolNFT v1 · #80826 · protein
Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3950 (1-(6-bromo-5-ethoxypyridin- 3-yl)-1,4-diazepane)
3U8N · Acetylcholine-binding protein: “Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3950…”. X-ray diffraction, 3 ligands (09S, NAG, SO4), 20 pockets (best druggability 0.85).…
- PDB
- 3U8N
- Type
- protein
- Length
- 4,040 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- 09S, NAG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 11 distinct chains · 8% helix, 49% 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 | 203 | 8% helix, 49% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 204 | 8% helix, 49% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 205 | 8% helix, 46% strand | P58154 |
| E, G, H, J, O, T | Acetylcholine-binding protein | protein | 201 | 8% helix, 49% strand | P58154 |
| F, K | Acetylcholine-binding protein | protein | 204 | 8% helix, 49% strand | P58154 |
| I, P, S | Acetylcholine-binding protein | protein | 203 | 8% helix, 49% strand | P58154 |
| L, R | Acetylcholine-binding protein | protein | 200 | 9% helix, 50% strand | P58154 |
| M | Acetylcholine-binding protein | protein | 202 | 8% helix, 49% strand | P58154 |
| N | Acetylcholine-binding protein | protein | 198 | 9% helix, 50% strand | P58154 |
| Q | Acetylcholine-binding protein | protein | 203 | 8% helix, 49% strand | P58154 |
Ligands and binding sites
- 09S · 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, J, A, G, N, T
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, G, H, M, N, P, T, Q, R, S
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 | 1113 | 0.85 | 0.86 | 117 | empty |
| 2 | 1160 | 0.85 | 0.85 | 118 | empty |
| 3 | 690 | 0.83 | 0.87 | 90 | empty |
| 4 | 263 | 0.73 | 0.87 | 41 | empty |
| 5 | 102 | 0.71 | 0.93 | 19 | 09S |
Interfaces
46 interfaces between chains.
- L–M · 1397 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1383 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1382 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1380 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1376 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3U8N · Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in… · the same entry in another collection · chain K against K, TM-score 1.00
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 3U8N · PDBe 3U8N · UniProt P58154
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