Research workbench
Crystals structure of the mutated protease domain of botulinum neurotoxin X (X4130B1).
Analyse Crystals structure of the mutated protease domain of botulinum neurotoxin X… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZ7
- Type
- protein
- Length
- 424 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type X
- EC
- 3.4.24.69
- UniProt
- P0DPK1
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Botulinum neurotoxin type X (EC 3.4.24.69) | protein | 424 | 29% helix, 22% strand | P0DPK1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.70 | 0.80 | 58 | EDO, GOL |
| 2 | 101 | 0.57 | 0.85 | 22 | EDO |
| 3 | 61 | 0.41 | 0.81 | 12 | empty |
| 4 | 113 | 0.38 | 0.74 | 25 | empty |
| 5 | 50 | 0.26 | 0.74 | 15 | empty |
Compared structures
- 7KZ7 · Crystals Structure of the Mutated Protease Domain of Botulinum Neurotoxin X (X4130B1). · the same entry in another collection · chain A against A, TM-score 1.00
- P0DPK1 · AlphaFold monomer V2.0 prediction for botulinum neurotoxin type X (P0DPK1) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P0DPK1
- Elsewhere: RCSB PDB 7KZ7 · PDBe 7KZ7 · UniProt P0DPK1
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