MolNFT v1 · #59777 · protein
Crystal structure of the catalytic domain of botulinum neurotoxin serotype a with inhibitory peptide rrgc
3C88 · Botulinum neurotoxin a light chain: “Crystal structure of the catalytic domain of botulinum neurotoxin serotype a with inhibitory peptide rrgc”. X-ray diffraction, 4 ligands (ZN, NA, SO4), 4 pockets (best druggability 0.53). MolNFT…
- PDB
- 3C88
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Botulinum neurotoxin a light chain; Inhibitor peptide rrgc
- EC
- 3.4.24.69
- UniProt
- P10845
- Ligands
- ZN, NA, SO4, NH2
- Pockets
- 4 · 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 a light chain (EC 3.4.24.69) | protein | 422 | 31% helix, 18% strand | P10845 |
| B | Inhibitor peptide rrgc | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.53 | 0.76 | 44 | SO4, NA |
| 2 | 73 | 0.35 | 0.76 | 15 | empty |
| 3 | 91 | 0.34 | 0.74 | 21 | empty |
| 4 | 52 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3C88 · Crystal structure of the catalytic domain of botulinum neurotoxin serotype A 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 P10845
- Elsewhere: RCSB PDB 3C88 · PDBe 3C88 · UniProt P10845
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