Research workbench
Small molecule inhibitor abs-143 bound to the botulinum neurotoxin serotype a light chain
Analyse Small molecule inhibitor abs-143 bound to the botulinum neurotoxin serotype a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V8P
- Type
- protein
- Length
- 790 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
- 90G, ZN
- Pockets
- 6 · best druggability 0.78
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 | 388 | 34% helix, 18% strand | P10845 |
| B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 402 | 33% helix, 18% strand | P10845 |
Ligands and binding sites
- 90G · N-[3-(4-chlorophenyl)-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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.78 | 0.80 | 64 | empty |
| 2 | 283 | 0.65 | 0.81 | 34 | 90G |
| 3 | 260 | 0.57 | 0.78 | 34 | 90G, ZN |
| 4 | 242 | 0.56 | 0.78 | 31 | empty |
| 5 | 209 | 0.53 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5V8P · 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 5V8P · PDBe 5V8P · UniProt P10845
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