Research workbench
Crystal structure of BONT/E lc-hn domain in complex with vhh jle-E5
Analyse Crystal structure of BONT/E lc-hn domain in complex with vhh jle-E5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K84
- Type
- protein
- Length
- 915 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type E; Jle-E5
- UniProt
- A0A6B4PXW0
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type E | protein | 793 | 46% helix, 15% strand | A0A6B4PXW0 |
| B | Jle-E5 | protein | 122 | 2% helix, 48% strand | — |
Ligands and binding sites
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 | 785 | 0.83 | 0.86 | 79 | empty |
| 2 | 148 | 0.65 | 0.87 | 27 | empty |
| 3 | 81 | 0.46 | 0.81 | 18 | empty |
| 4 | 62 | 0.34 | 0.77 | 15 | empty |
| 5 | 93 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7K84 · Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A6B4PXW0
- Elsewhere: RCSB PDB 7K84 · PDBe 7K84 · UniProt A0A6B4PXW0
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