Research workbench
Crystal structure of BONT/B receptor-binding domain in complex with vhh jli-H11
Analyse Crystal structure of BONT/B receptor-binding domain in complex with vhh jli-H11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UC6
- Type
- protein
- Length
- 1,080 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Jli-H11
- EC
- 3.4.24.69
- UniProt
- P10844
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 414 | 5% helix, 45% strand | P10844 |
| C | Jli-H11 | protein | 126 | 15% helix, 46% strand | — |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 412 | 6% helix, 45% strand | P10844 |
| D | Jli-H11 | protein | 128 | 13% helix, 45% strand | — |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.69 | 0.81 | 48 | empty |
| 2 | 361 | 0.68 | 0.81 | 47 | empty |
| 3 | 441 | 0.62 | 0.76 | 58 | empty |
| 4 | 82 | 0.61 | 0.89 | 22 | empty |
| 5 | 457 | 0.60 | 0.75 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–C · 775 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 771 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 81 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UC6 · Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11 · 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
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 6UC6 · PDBe 6UC6 · UniProt P10844
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