Research workbench
Crystal structure of the botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain
Analyse Crystal structure of the botulinum neurotoxin type B complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NP0
- Type
- protein
- Length
- 1,304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Synaptotagmin-2
- EC
- 3.4.24.69
- UniProt
- P10844, P46097
- Ligands
- CA, ZN, CL
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 1289 | 29% helix, 24% strand | P10844 |
| B | Synaptotagmin-2 | protein | 15 | 73% helix, 0% strand | P46097 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 106 | CA |
| 2 | 289 | 0.76 | 0.88 | 43 | empty |
| 3 | 449 | 0.69 | 0.80 | 49 | empty |
| 4 | 282 | 0.64 | 0.81 | 35 | empty |
| 5 | 63 | 0.60 | 0.91 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 641 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2NP0 · Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II… · the same entry in another collection · chain B against B, TM-score 1.00
- P46097 · AlphaFold monomer V2.0 prediction for synaptotagmin-2 (P46097) · a predicted model of the same protein · chain B against A, TM-score 0.72
- 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 0.67
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
- Every structure of UniProt P46097
- Elsewhere: RCSB PDB 2NP0 · PDBe 2NP0 · UniProt P10844 · UniProt P46097
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.