MolNFT v1 · #95523 · protein
Binding domain of botulinum neurotoxin dc in complex with rat synaptotagmin II
4ISR: “Binding domain of botulinum neurotoxin dc in complex with rat synaptotagmin II”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.77). MolNFT v1 #95523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
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