Research workbench
Crystal structure of BONT/B receptor-binding domain in complex with vhh jli-G10
Analyse Crystal structure of BONT/B receptor-binding domain in complex with vhh jli-G10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UHT
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Jli-G10
- EC
- 3.4.24.69
- UniProt
- P10844
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 431 | 6% helix, 43% strand | P10844 |
| B | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 421 | 6% helix, 44% strand | P10844 |
| C | Jli-G10 | protein | 124 | 7% helix, 48% strand | — |
| D | Jli-G10 | protein | 130 | 12% helix, 48% strand | — |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.74 | 0.80 | 84 | empty |
| 2 | 540 | 0.73 | 0.81 | 54 | empty |
| 3 | 307 | 0.63 | 0.80 | 40 | empty |
| 4 | 133 | 0.62 | 0.86 | 27 | empty |
| 5 | 82 | 0.60 | 0.89 | 23 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1047 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 581 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6UHT · Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10 · 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 B 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 6UHT · PDBe 6UHT · UniProt P10844
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