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The pore structure of clostridium perfringens epsilon toxin

Analyse The pore structure of clostridium perfringens epsilon toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RB9
Type: protein
Length: 1,736 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epsilon-toxin type B
UniProt: Q02307
Pockets: 19 · best druggability 0.66

Structure

electron microscopy · 1 distinct chain · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Epsilon-toxin type B	protein	248	7% helix, 48% strand	Q02307

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.66	0.84	24	empty
2	240	0.65	0.83	27	empty
3	232	0.65	0.83	27	empty
4	232	0.65	0.83	32	empty
5	208	0.65	0.83	26	empty

Interfaces

14 interfaces between chains.

B–C · 2855 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 2853 Å² buried · 56 hydrogen bonds · protein-protein
A–G · 2852 Å² buried · 56 hydrogen bonds · protein-protein
F–G · 2850 Å² buried · 56 hydrogen bonds · protein-protein
E–F · 2848 Å² buried · 56 hydrogen bonds · protein-protein

Compared structures

6RB9 · The pore structure of Clostridium perfringens epsilon toxin · the same entry in another collection · chain G against G, TM-score 1.00
Q02307 · AlphaFold monomer V2.0 prediction for epsilon-toxin type B (Q02307) · a predicted model of the same protein · chain E against A, TM-score 0.39

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 Q02307
Elsewhere: RCSB PDB 6RB9 · PDBe 6RB9 · UniProt Q02307

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