Research workbench
Crystal structure of clostridium botulinum neurotoxin B complexed with a trisaccharide
Analyse Crystal structure of clostridium botulinum neurotoxin B complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F31
- Type
- protein
- Length
- 1,280 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B
- EC
- 3.4.24.69
- UniProt
- P10844
- Ligands
- GLC, GLA, SIA, ZN, SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 1280 | 30% helix, 24% strand | P10844 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.79 | 0.82 | 67 | SO4 |
| 2 | 280 | 0.79 | 0.90 | 35 | empty |
| 3 | 491 | 0.71 | 0.81 | 59 | empty |
| 4 | 536 | 0.68 | 0.78 | 46 | empty |
| 5 | 515 | 0.65 | 0.77 | 42 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1F31 · Crystal structure of clostridium botulinum neurotoxin B complexed with a trisaccharide · 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 0.66
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 1F31 · PDBe 1F31 · UniProt P10844
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