MolNFT v1 · #136950 · protein
Small molecule inhibitor abs-143 bound to the botulinum neurotoxin serotype a light chain
5V8U · Botulinum neurotoxin type a: “Small molecule inhibitor abs-143 bound to the botulinum neurotoxin serotype a light chain”. X-ray diffraction, 2 ligands (90M, ZN), 9 pockets (best druggability 0.77). MolNFT v1 #136950 on GenesisL1: 3D…
- PDB
- 5V8U
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a
- EC
- 3.4.24.69
- UniProt
- P10845
- Ligands
- 90M, ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 389 | 33% helix, 19% strand | P10845 |
| B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 385 | 32% helix, 18% strand | P10845 |
Ligands and binding sites
- 90M · N-[3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-yl]-2-sulfanylacetamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.77 | 0.80 | 56 | empty |
| 2 | 351 | 0.61 | 0.78 | 46 | ZN, 90M |
| 3 | 218 | 0.59 | 0.80 | 33 | 90M |
| 4 | 264 | 0.58 | 0.78 | 44 | empty |
| 5 | 200 | 0.58 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1837 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5V8U · Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain · the same entry in another collection · chain A against A, 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 P10845
- Elsewhere: RCSB PDB 5V8U · PDBe 5V8U · UniProt P10845
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