MolNFT v1 · #55325 · protein
Clostridium perfringens delta-toxin
2YGT · Delta toxin: “Clostridium perfringens delta-toxin”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.38). MolNFT v1 #55325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YGT
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta toxin
- UniProt
- B8QGZ7
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta toxin | protein | 282 | 4% helix, 59% strand | B8QGZ7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.38 | 0.78 | 19 | empty |
Compared structures
- 2YGT · Clostridium perfringens delta-toxin · 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 B8QGZ7
- Elsewhere: RCSB PDB 2YGT · PDBe 2YGT · UniProt B8QGZ7
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