MolNFT v1 · #179517 · protein
Crystal structure of BONT/E lc-hn domain in complex with vhh jle-E9
7K7Y · Botulinum neurotoxin type E: “Crystal structure of BONT/E lc-hn domain in complex with vhh jle-E9”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #179517 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7K7Y
- Type
- protein
- Length
- 3,625 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type E; Jle-E9
- UniProt
- A0A6B4PXW0
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type E | protein | 789 | 44% helix, 15% strand | A0A6B4PXW0 |
| D | Jle-E9 | protein | 125 | 2% helix, 42% strand | — |
| E | Botulinum neurotoxin type E | protein | 775 | 44% helix, 15% strand | A0A6B4PXW0 |
| G | Botulinum neurotoxin type E | protein | 789 | 44% helix, 14% strand | A0A6B4PXW0 |
| B | Botulinum neurotoxin type E | protein | 783 | 44% helix, 15% strand | A0A6B4PXW0 |
| C, H | Jle-E9 | protein | 123 | 2% helix, 43% strand | — |
| F | Jle-E9 | protein | 118 | 3% helix, 42% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 99 | empty |
| 2 | 1031 | 0.85 | 0.86 | 90 | empty |
| 3 | 1071 | 0.84 | 0.85 | 105 | empty |
| 4 | 997 | 0.83 | 0.84 | 96 | empty |
| 5 | 1136 | 0.74 | 0.77 | 89 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1019 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 951 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 947 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 946 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 608 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7K7Y · Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E9 · 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 7K7Y · PDBe 7K7Y · UniProt A0A6B4PXW0
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