MolNFT v1 · #101698 · protein
NS9283 bound to ls-achbp
4NZB · Acetylcholine-binding protein: “NS9283 bound to ls-achbp”. X-ray diffraction, 4 ligands (NSE, NAG, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #101698 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NZB
- Type
- protein
- Length
- 2,963 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- P58154
- Ligands
- NSE, NAG, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, E, A, B, C, H, J, L, N, O | Acetylcholine-binding protein | protein | 198 | 9% helix, 49% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 197 | 9% helix, 50% strand | P58154 |
| F | Acetylcholine-binding protein | protein | 200 | 9% helix, 49% strand | P58154 |
| I | Acetylcholine-binding protein | protein | 195 | 9% helix, 50% strand | P58154 |
| K | Acetylcholine-binding protein | protein | 197 | 9% helix, 49% strand | P58154 |
| M | Acetylcholine-binding protein | protein | 194 | 9% helix, 51% strand | P58154 |
Ligands and binding sites
- NSE · 3-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]benzonitrile · ligand · 6 copies · chains E, A, B, C, I, J, K, L, M, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G, D
- SO4 · Sulfate ion · ion · 20 copies · chains G, F, H, D, E, A, B, C, J, I, M
- CL · Chloride ion · ion · 4 copies · chains A, K, L, M, N
- ACT · Acetate ion · additive · 12 copies · chains G, F, H, D, C, A, J, L, K, O
- 1PE · Pentaethylene glycol · additive · 8 copies · chains G, D, E, A, B, C, H, I
- GOL · Glycerol · additive · chains 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 | 601 | 0.81 | 0.87 | 53 | ACT |
| 2 | 1049 | 0.80 | 0.81 | 82 | ACT |
| 3 | 476 | 0.76 | 0.84 | 42 | empty |
| 4 | 512 | 0.73 | 0.82 | 52 | SO4 |
| 5 | 512 | 0.73 | 0.82 | 48 | ACT |
Interfaces
20 interfaces between chains.
- K–O · 1344 Ų buried · 18 hydrogen bonds · protein-protein
- F–J · 1316 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1307 Ų buried · 17 hydrogen bonds · protein-protein
- G–F · 1273 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1257 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4NZB · NS9283 bound to Ls-AChBP · 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 4NZB · PDBe 4NZB · UniProt P58154
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