MolNFT v1 · #54186 · protein

Clostridium perfringens enterotoxin

2XH6 · Heat-labile enterotoxin B chain: “Clostridium perfringens enterotoxin”. X-ray diffraction, 4 pockets (best druggability 0.85). MolNFT v1 #54186 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XH6
Type: protein
Length: 853 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat-labile enterotoxin B chain
UniProt: P01558
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Heat-labile enterotoxin B chain	protein	285	11% helix, 54% strand	P01558
B	Heat-labile enterotoxin B chain	protein	283	11% helix, 54% strand	P01558

Ligands and binding sites

DIO · 1,4-diethylene dioxide · additive · 3 copies · chains A, C
BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, C, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1026	0.85	0.86	139	DIO, BOG
2	61	0.52	0.87	21	empty
3	112	0.52	0.82	27	empty
4	94	0.42	0.78	20	empty

Interfaces

3 interfaces between chains.

A–C · 957 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 917 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 898 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2XH6 · Clostridium perfringens enterotoxin · the same entry in another collection · chain A against A, TM-score 1.00
P01558 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P01558) · a predicted model of the same protein · chain B 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 P01558
Elsewhere: RCSB PDB 2XH6 · PDBe 2XH6 · UniProt P01558

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