MolNFT v1 · #147932 · protein
Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
6ES1 · Botulinum neurotoxin type a: “Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human…”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #147932 on GenesisL1: 3D…
- 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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