MolNFT v1 · #127562 · protein
Crystal structure of the tetanus neurotoxin in complex with GD1A
5N0B · Tetanus toxin: “Crystal structure of the tetanus neurotoxin in complex with GD1A”. X-ray diffraction, 5 ligands (GAL, SIA, BGC), 20 pockets (best druggability 0.83). MolNFT v1 #127562 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N0B
- Type
- protein
- Length
- 1,280 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
- GAL, SIA, BGC, NGA, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetanus toxin (EC 3.4.24.68) | protein | 1280 | 30% helix, 24% strand | P04958 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.83 | 0.84 | 76 | ZN, PEG |
| 2 | 1165 | 0.79 | 0.81 | 102 | empty |
| 3 | 329 | 0.65 | 0.80 | 40 | empty |
| 4 | 125 | 0.63 | 0.86 | 27 | empty |
| 5 | 96 | 0.59 | 0.87 | 19 | empty |
Modifications
Observed in the structure: 2 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 5N0B · PDBe 5N0B · UniProt P04958
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