Research workbench
Binding domain of botulinum neurotoxin dc in complex with rat synaptotagmin II
Analyse Binding domain of botulinum neurotoxin dc in complex with rat synaptotagmin II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ISR
- Type
- protein
- Length
- 1,288 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurotoxin; Synaptotagmin-2
- UniProt
- Q9LBR1, P29101
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurotoxin | protein | 414 | 7% helix, 49% strand | Q9LBR1 |
| B | Neurotoxin | protein | 413 | 8% helix, 49% strand | Q9LBR1 |
| C | Neurotoxin | protein | 413 | 8% helix, 49% strand | Q9LBR1 |
| D, E, F | Synaptotagmin-2 | protein | 16 | 75% helix, 0% strand | P29101 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.77 | 0.79 | 104 | empty |
| 2 | 257 | 0.56 | 0.77 | 41 | empty |
| 3 | 253 | 0.55 | 0.77 | 40 | empty |
| 4 | 236 | 0.55 | 0.77 | 38 | empty |
| 5 | 75 | 0.51 | 0.85 | 23 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 809 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 738 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 727 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 716 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 617 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ISR · Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II · the same entry in another collection · chain C against C, TM-score 1.00
- P29101 · AlphaFold monomer V2.0 prediction for synaptotagmin-2 (P29101) · a predicted model of the same protein · chain D against A, TM-score 0.65
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 Q9LBR1
- Every structure of UniProt P29101
- Elsewhere: RCSB PDB 4ISR · PDBe 4ISR · UniProt Q9LBR1 · UniProt P29101
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.