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Crystal structure of the catalytic domain of botulinum neurotoxin BONT/A C134S mutant with covalent inhibitor that modifies cys-165 causing disorder in 167-174 stretch
Analyse Crystal structure of the catalytic domain of botulinum neurotoxin BONT/A C134S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KTX
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Peptide inhibitor mpt-dpp-arg-G-leu-NH2
- EC
- 3.4.24.69
- UniProt
- A5HZZ9
- Ligands
- MPT, ZN, NH2, SO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin a light chain (EC 3.4.24.69) | protein | 428 | 31% helix, 16% strand | A5HZZ9 |
| B | Peptide inhibitor mpt-dpp-arg-G-leu-NH2 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains A, B
- ZN · Zinc ion · metal · chains A, B
- NH2 · Amino group · ion · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PGO · S-1,2-propanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.81 | 0.84 | 81 | MPT |
| 2 | 131 | 0.41 | 0.75 | 22 | empty |
| 3 | 56 | 0.31 | 0.75 | 12 | empty |
| 4 | 67 | 0.29 | 0.73 | 12 | empty |
| 5 | 61 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 4KTX · Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant… · 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 A5HZZ9
- Elsewhere: RCSB PDB 4KTX · PDBe 4KTX · UniProt A5HZZ9
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