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Crystal structure of the catalytic domain of botulinum neurotoxin serotype a with a substrate analog peptide
Analyse Crystal structure of the catalytic domain of 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
- 3DDB
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Synaptosomal-associated protein 25
- EC
- 3.4.24.69
- UniProt
- A5HZZ9
- Ligands
- ZN, SO4, NH2
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 423 | 31% helix, 18% strand | A5HZZ9 |
| B | Synaptosomal-associated protein 25 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.53 | 0.77 | 34 | SO4 |
| 2 | 63 | 0.37 | 0.79 | 21 | empty |
| 3 | 70 | 0.34 | 0.76 | 15 | empty |
| 4 | 59 | 0.31 | 0.75 | 12 | empty |
| 5 | 50 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3DDB · Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a… · 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 A5HZZ9
- Elsewhere: RCSB PDB 3DDB · PDBe 3DDB · UniProt A5HZZ9
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