Research workbench
Structure of botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1A
Analyse Structure of botulinum neurotoxin B binding domain in complex with both… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KBB
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Synaptotagmin-2
- EC
- 3.4.24.69
- UniProt
- P10844, P46097
- Ligands
- GAL, SIA, BGC, NGA, MG, CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 417 | 5% helix, 44% strand | P10844 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 417 | 6% helix, 45% strand | P10844 |
| C | Synaptotagmin-2 | protein | 15 | 80% helix, 0% strand | P46097 |
| D | Synaptotagmin-2 | protein | 18 | 83% helix, 0% strand | P46097 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.74 | 0.78 | 84 | GAL |
| 2 | 311 | 0.64 | 0.80 | 43 | CL |
| 3 | 304 | 0.63 | 0.80 | 46 | CL |
| 4 | 114 | 0.60 | 0.86 | 23 | empty |
| 5 | 78 | 0.58 | 0.88 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 757 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4KBB · Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II… · the same entry in another collection · chain A against A, TM-score 1.00
- P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P46097 · AlphaFold monomer V2.0 prediction for synaptotagmin-2 (P46097) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P10844
- Every structure of UniProt P46097
- Elsewhere: RCSB PDB 4KBB · PDBe 4KBB · UniProt P10844 · UniProt P46097
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