Research workbench
Crystal structure of the botulinum neurotoxin a receptor-binding domain in complex with the luminal domain of SV2C
Analyse Crystal structure of the botulinum neurotoxin a receptor-binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JRA
- Type
- protein
- Length
- 1,005 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
- NA, CL
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 416 | 5% helix, 47% strand | P10845 |
| B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 413 | 6% helix, 44% strand | P10845 |
| C | Synaptic vesicle glycoprotein 2C | protein | 83 | 4% helix, 47% strand | Q496J9 |
| D | Synaptic vesicle glycoprotein 2C | protein | 93 | 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.69 | 0.82 | 30 | CL |
| 2 | 632 | 0.68 | 0.77 | 47 | empty |
| 3 | 298 | 0.68 | 0.83 | 35 | empty |
| 4 | 75 | 0.55 | 0.86 | 20 | empty |
| 5 | 73 | 0.46 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 619 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 563 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 334 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4JRA · CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH… · 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 C 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 4JRA · PDBe 4JRA · UniProt P10845 · UniProt Q496J9
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