Research workbench
Crystal structure of BONT/B receptor-binding domain in complex with vhh jlk-G12
Analyse Crystal structure of BONT/B receptor-binding domain in complex with vhh jlk-G12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UFT
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Jlk-G12
- EC
- 3.4.24.69
- UniProt
- P10844
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 423 | 5% helix, 45% strand | P10844 |
| B | Jlk-G12 | protein | 128 | 7% helix, 47% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.63 | 0.93 | 22 | empty |
| 2 | 263 | 0.61 | 0.80 | 36 | empty |
| 3 | 64 | 0.48 | 0.84 | 13 | empty |
| 4 | 57 | 0.47 | 0.85 | 16 | empty |
| 5 | 70 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6UFT · Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLK-G12 · 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 0.97
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 P10844
- Elsewhere: RCSB PDB 6UFT · PDBe 6UFT · UniProt P10844
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