Research workbench
Crystal structure of the catalytic domain of botulinum neurotoxin serotype a with a novel cyclic peptide inhibitor
Analyse Crystal structure of the catalytic domain of botulinum neurotoxin serotype a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZJX
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a; Circular peptide inhibitor
- EC
- 3.4.24.69
- UniProt
- P10845
- Ligands
- ZN, SO4, NH2
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 417 | 31% helix, 19% strand | P10845 |
| B | Circular peptide inhibitor | protein | 8 | 38% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
- NH2 · Amino group · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.53 | 0.78 | 33 | SO4 |
| 2 | 94 | 0.35 | 0.74 | 22 | SO4 |
| 3 | 67 | 0.33 | 0.76 | 13 | empty |
| 4 | 57 | 0.32 | 0.76 | 15 | empty |
| 5 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 679 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4ZJX · Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel… · 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 P10845
- Elsewhere: RCSB PDB 4ZJX · PDBe 4ZJX · UniProt P10845
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