Research workbench
Structure of a functional derivative of clostridium botulinum neurotoxin type B
Analyse Structure of a functional derivative of clostridium botulinum neurotoxin type B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XHL
- Type
- protein
- Length
- 840 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin B light chain; Botulinum neurotoxin B heavy chain
- EC
- 3.4.24.69
- UniProt
- P10844
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin B light chain (EC 3.4.24.69) | protein | 430 | 31% helix, 19% strand | P10844 |
| B | Botulinum neurotoxin B heavy chain | protein | 410 | 53% helix, 8% strand | P10844 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.80 | 0.83 | 66 | empty |
| 2 | 624 | 0.76 | 0.82 | 70 | empty |
| 3 | 321 | 0.59 | 0.77 | 43 | empty |
| 4 | 157 | 0.57 | 0.81 | 26 | empty |
| 5 | 88 | 0.49 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 5498 Ų buried · 91 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2XHL · Structure of a functional derivative of Clostridium botulinum neurotoxin type B · the same entry in another collection · chain A against A, TM-score 1.00
- P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P10844
- Elsewhere: RCSB PDB 2XHL · PDBe 2XHL · UniProt P10844
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