Research workbench
Botulinum neurotoxin type B light chain complexed with nanobodies jlj- G3 and jne-B10
Analyse Botulinum neurotoxin type B light chain complexed with nanobodies jlj- G3 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T5F
- Type
- protein
- Length
- 1,297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type B; Jlj-G3; Jne-B10
- EC
- 3.4.24.69
- UniProt
- P10844
- Ligands
- ZN, IOD
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 421 | 33% helix, 16% strand | P10844 |
| D | Botulinum neurotoxin type B (EC 3.4.24.69) | protein | 420 | 34% helix, 17% strand | P10844 |
| C | Jlj-G3 | protein | 115 | 5% helix, 48% strand | — |
| B | Jne-B10 | protein | 117 | 5% helix, 48% strand | — |
| E | Jne-B10 | protein | 110 | 8% helix, 49% strand | — |
| F | Jlj-G3 | protein | 114 | 5% helix, 48% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D
- IOD · Iodide ion · ion · 6 copies · chains A, D, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.73 | 0.77 | 78 | empty |
| 2 | 453 | 0.68 | 0.80 | 41 | empty |
| 3 | 407 | 0.67 | 0.80 | 46 | ZN |
| 4 | 167 | 0.64 | 0.85 | 29 | empty |
| 5 | 166 | 0.63 | 0.84 | 29 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1014 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 676 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 648 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 394 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7T5F · Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10 · the same entry in another collection · chain F against F, TM-score 1.00
- P10844 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type B (P10844) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 7T5F · PDBe 7T5F · UniProt P10844
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