Research workbench
A common binding site for disialyllactose and a tri-peptide in the C- fragment of tetanus neurotoxin
Analyse A common binding site for disialyllactose and a tri-peptide in the C- fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYN
- Type
- protein
- Length
- 441 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetanus toxin
- EC
- 3.4.24.68
- UniProt
- P04958
- Ligands
- SIA, BGC, GLA
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetanus toxin (EC 3.4.24.68) | protein | 441 | 7% helix, 44% strand | P04958 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar
- GLA · alpha-D-galactopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.48 | 0.76 | 24 | empty |
| 2 | 161 | 0.48 | 0.77 | 24 | empty |
| 3 | 55 | 0.37 | 0.80 | 13 | empty |
| 4 | 58 | 0.29 | 0.75 | 14 | empty |
Compared structures
- 1YYN · A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus… · the same entry in another collection · chain A against A, TM-score 1.00
- P04958 · AlphaFold monomer V2.0 prediction for tetanus toxin (P04958) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04958
- Elsewhere: RCSB PDB 1YYN · PDBe 1YYN · UniProt P04958
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