Research workbench
Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
Analyse Crystal structure of the binding domain from botulinum neurotoxin A2 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ES1
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a; Synaptic vesicle glycoprotein 2C
- EC
- 3.4.24.69
- UniProt
- Q45894, Q496J9
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 420 | 7% helix, 46% strand | Q45894 |
| B | Synaptic vesicle glycoprotein 2C | protein | 95 | 3% helix, 62% strand | Q496J9 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.69 | 0.83 | 33 | empty |
| 2 | 205 | 0.48 | 0.75 | 39 | ACT |
| 3 | 139 | 0.41 | 0.74 | 20 | empty |
| 4 | 118 | 0.38 | 0.75 | 26 | empty |
| 5 | 98 | 0.37 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ES1 · Crystal structure of the binding domain from botulinum neurotoxin A2 bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q45894 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type A2 (Q45894) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q496J9 · AlphaFold monomer V2.0 prediction for synaptic vesicle glycoprotein 2C (Q496J9) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q45894
- Every structure of UniProt Q496J9
- Elsewhere: RCSB PDB 6ES1 · PDBe 6ES1 · UniProt Q45894 · UniProt Q496J9
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