Research workbench
Botulism neurooxin light chain a app form
Analyse Botulism neurooxin light chain a app form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KYH
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BONT/A1
- UniProt
- C6K838
- Ligands
- XBM, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | BONT/A1 | protein | 385 | 29% helix, 16% strand | C6K838 |
Ligands and binding sites
- XBM · N-[(3,5-dichlorophenyl)sulfonyl]-L-phenylalanyl-N-hydroxy-L-valinamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.83 | 0.84 | 96 | empty |
| 2 | 484 | 0.69 | 0.79 | 38 | empty |
| 3 | 405 | 0.63 | 0.78 | 47 | XBM |
| 4 | 313 | 0.62 | 0.79 | 41 | XBM |
| 5 | 172 | 0.59 | 0.82 | 23 | XBM |
Interfaces
4 interfaces between chains.
- B–C · 796 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 595 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 327 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7KYH · Botulism Neurooxin Light Chain A app form · 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 C6K838
- Elsewhere: RCSB PDB 7KYH · PDBe 7KYH · UniProt C6K838
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