MolNFT v1 · #127184 · protein
Crystal structure of the BONT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C
5MOY · Botulinum neurotoxin type a: “Crystal structure of the BONT/A2 receptor-binding domain in complex with the luminal domain of its neuronal…”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #127184 on GenesisL1: 3D…
- PDB
- 5MOY
- Type
- protein
- Length
- 517 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
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 414 | 7% helix, 45% strand | Q45894 |
| B | Synaptic vesicle glycoprotein 2C | protein | 103 | 3% helix, 60% strand | Q496J9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.61 | 0.77 | 29 | 2PE |
| 2 | 121 | 0.43 | 0.77 | 23 | empty |
| 3 | 149 | 0.40 | 0.73 | 19 | empty |
| 4 | 93 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MOY · Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal… · 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 0.98
- 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 0.88
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 5MOY · PDBe 5MOY · UniProt Q45894 · UniProt Q496J9
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