MolNFT v1 · #76815 · protein
Crystal structure of the protease domain of botulinum neurotoxin serotype a with a peptide inhibitor rygc
3QW6 · Botulinum neurotoxin type a: “Crystal structure of the protease domain of botulinum neurotoxin serotype a with a peptide inhibitor rygc”. X-ray diffraction, 4 ligands (ZN, NA, SO4), 4 pockets (best druggability 0.56). MolNFT v1…
- PDB
- 3QW6
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin type a; Inhibitory peptide rygc
- EC
- 3.4.24.69
- UniProt
- A5HZZ9
- Ligands
- ZN, NA, SO4, NH2
- Pockets
- 4 · best druggability 0.56
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 | 422 | 31% helix, 18% strand | A5HZZ9 |
| B | Inhibitory peptide rygc | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- NA · Sodium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.56 | 0.77 | 45 | SO4, NA |
| 2 | 81 | 0.51 | 0.84 | 15 | empty |
| 3 | 88 | 0.34 | 0.75 | 23 | empty |
| 4 | 50 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3QW6 · Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a… · 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 3QW6 · PDBe 3QW6 · UniProt A5HZZ9
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