Research workbench
The hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B
Analyse The hc fragment of tetanus toxin complexed with an analogue of its ganglioside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FV3
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetanus toxin heavy chain
- UniProt
- P04958
- Ligands
- CEQ, GAL, SIA, BGC, NGA, SLB, PO4
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tetanus toxin heavy chain | protein | 451 | 8% helix, 45% strand | P04958 |
Ligands and binding sites
- CEQ · Ethyl-trimethyl-silane · ligand · 2 copies
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SLB · N-acetyl-beta-neuraminic acid · sugar · 2 copies · chains B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.56 | 0.85 | 27 | empty |
| 2 | 168 | 0.50 | 0.78 | 24 | empty |
| 3 | 162 | 0.48 | 0.77 | 24 | empty |
| 4 | 148 | 0.47 | 0.77 | 34 | empty |
| 5 | 171 | 0.45 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1FV3 · The hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor… · 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 0.98
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 1FV3 · PDBe 1FV3 · UniProt P04958
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