MolNFT v1 · #60844 · protein
Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with snap-25 substrate peptide
3D3X · Type E botulinum toxin: “Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with snap-25 substrate…”. X-ray diffraction, 3 ligands (ZN, SO4, NH2), 6 pockets (best druggability 0.82). MolNFT v1 #60844 on…
- PDB
- 3D3X
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type E botulinum toxin; Snap-25 substrate peptide
- UniProt
- Q9K395
- Ligands
- ZN, SO4, NH2
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type E botulinum toxin | protein | 407 | 35% helix, 17% strand | Q9K395 |
| B | Type E botulinum toxin | protein | 407 | 34% helix, 17% strand | Q9K395 |
| C | Snap-25 substrate peptide | protein | 3 | 0% helix, 0% strand | — |
| D | Snap-25 substrate peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- NH2 · Amino group · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.82 | 0.83 | 100 | empty |
| 2 | 263 | 0.53 | 0.76 | 44 | NH2, SO4 |
| 3 | 175 | 0.46 | 0.75 | 25 | SO4 |
| 4 | 85 | 0.37 | 0.76 | 25 | empty |
| 5 | 77 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1298 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 534 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3D3X · Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with… · 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 Q9K395
- Elsewhere: RCSB PDB 3D3X · PDBe 3D3X · UniProt Q9K395
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