MolNFT v1 · #123493 · protein
Receptor binding domain of botulinum neurotoxin a in complex with human glycosylated SV2C
5JLV · Botulinum neurotoxin type a: “Receptor binding domain of botulinum neurotoxin a in complex with human glycosylated SV2C”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 11 pockets (best druggability 0.56). MolNFT v1 #123493 on…
- PDB
- 5JLV
- Type
- protein
- Length
- 1,038 residues
- Chains
- 4
- 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
- P10845, Q496J9
- Ligands
- NAG, FUC, BMA, PO4
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 425 | 8% helix, 46% strand | P10845 |
| C | Synaptic vesicle glycoprotein 2C | protein | 97 | 3% helix, 62% strand | Q496J9 |
| D | Synaptic vesicle glycoprotein 2C | protein | 91 | 3% helix, 67% strand | Q496J9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.56 | 0.80 | 22 | empty |
| 2 | 166 | 0.52 | 0.79 | 29 | ACT |
| 3 | 121 | 0.50 | 0.80 | 26 | empty |
| 4 | 186 | 0.46 | 0.75 | 26 | empty |
| 5 | 152 | 0.43 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–C · 621 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 617 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 472 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 5JLV · Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C · the same entry in another collection · chain A against A, TM-score 1.00
- Q496J9 · AlphaFold monomer V2.0 prediction for synaptic vesicle glycoprotein 2C (Q496J9) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P10845
- Every structure of UniProt Q496J9
- Elsewhere: RCSB PDB 5JLV · PDBe 5JLV · UniProt P10845 · UniProt Q496J9
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