Research workbench

Cholera toxin B-pentamer with ligand bmsc-0011

Analyse Cholera toxin B-pentamer with ligand bmsc-0011 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JR0
Type: protein
Length: 515 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholera toxin B subunit
UniProt: P01556
Ligands: A24
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F, G, H	Cholera toxin B subunit	protein	103	24% helix, 37% strand	P01556

Ligands and binding sites

A24 · (3-nitro-5-(2-morpholin-4-yl-ethylaminocarbonyl)phenyl)-galactopyranoside · ligand · 5 copies · chains D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.73	0.77	41	empty
2	58	0.44	0.83	18	empty
3	53	0.37	0.80	18	empty
4	52	0.29	0.76	14	empty
5	52	0.27	0.74	13	A24

Interfaces

5 interfaces between chains.

D–E · 1317 Å² buried · 25 hydrogen bonds · protein-protein
D–H · 1317 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 1296 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1281 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1262 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1JR0 · Cholera toxin B-pentamer with ligand bmsc-0011 · the same entry in another collection · chain H against H, TM-score 1.00
P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P01556
Elsewhere: RCSB PDB 1JR0 · PDBe 1JR0 · UniProt P01556

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