Research workbench

Mutant toxin in 'native' space group

Analyse Mutant toxin in 'native' space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DIM
Type: protein
Length: 465 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Perfringolysin O
UniProt: P0C2E9
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Perfringolysin O	protein	465	21% helix, 41% strand	P0C2E9

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.66	0.82	38	empty
2	138	0.61	0.85	22	empty
3	62	0.35	0.77	14	empty

Compared structures

5DIM · Mutant toxin in 'native' space group · the same entry in another collection · chain A against A, TM-score 1.00
P0C2E9 · AlphaFold monomer V2.0 prediction for perfringolysin O (P0C2E9) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P0C2E9
Elsewhere: RCSB PDB 5DIM · PDBe 5DIM · UniProt P0C2E9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.