Research workbench
Crystal structure of the tetanus neurotoxin in complex with GM1A
Analyse Crystal structure of the tetanus neurotoxin in complex with GM1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N0C
- Type
- protein
- Length
- 2,579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetanus toxin
- EC
- 3.4.24.68
- UniProt
- P04958
- Ligands
- GAL, BGC, NGA, SIA, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetanus toxin (EC 3.4.24.68) | protein | 1293 | 30% helix, 25% strand | P04958 |
| B | Tetanus toxin (EC 3.4.24.68) | protein | 1286 | 29% helix, 25% strand | P04958 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.83 | 0.84 | 81 | ZN |
| 2 | 1182 | 0.82 | 0.83 | 77 | ZN |
| 3 | 1020 | 0.82 | 0.83 | 100 | empty |
| 4 | 1075 | 0.81 | 0.82 | 92 | empty |
| 5 | 559 | 0.68 | 0.78 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 1452 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 5N0C · PDBe 5N0C · UniProt P04958
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