Research workbench
Crystal structure of BONT/B receptor-binding domain in complex with vhh jlo-G11
Analyse Crystal structure of BONT/B receptor-binding domain in complex with vhh jlo-G11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UL4
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Vhh jlo-G11
- EC
- 3.4.24.69
- UniProt
- P10844
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 428 | 5% helix, 45% strand | P10844 |
| B | Vhh jlo-G11 | protein | 125 | 2% helix, 40% strand | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.67 | 0.95 | 21 | empty |
| 2 | 66 | 0.64 | 0.93 | 18 | empty |
| 3 | 258 | 0.61 | 0.80 | 32 | empty |
| 4 | 67 | 0.49 | 0.84 | 18 | empty |
| 5 | 99 | 0.40 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6UL4 · Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLO-G11 · 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 6UL4 · PDBe 6UL4 · UniProt P10844
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