MolNFT v1 · #84410 · protein
Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside
3ZJX · Epsilon-toxin: “Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.64). MolNFT v1 #84410 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ZJX
- Type
- protein
- Length
- 1,101 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epsilon-toxin
- UniProt
- E7D8R1
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epsilon-toxin | protein | 277 | 11% helix, 57% strand | E7D8R1 |
| B, C | Epsilon-toxin | protein | 276 | 11% helix, 57% strand | E7D8R1 |
| D | Epsilon-toxin | protein | 272 | 10% helix, 57% strand | E7D8R1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.64 | 0.87 | 24 | empty |
| 2 | 93 | 0.54 | 0.84 | 22 | empty |
| 3 | 99 | 0.53 | 0.83 | 22 | empty |
| 4 | 58 | 0.53 | 0.87 | 16 | BOG |
| 5 | 58 | 0.52 | 0.87 | 19 | BOG |
Interfaces
4 interfaces between chains.
- A–C · 366 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 254 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 232 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZJX · Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside · 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 E7D8R1
- Elsewhere: RCSB PDB 3ZJX · PDBe 3ZJX · UniProt E7D8R1
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