MolNFT v2 · #11592 · protein

Cholera toxin B-pentamer with ligand bmsc-0011

1JR0 · cholera toxin B subunit: “Cholera toxin B-pentamer with ligand bmsc-0011”. X-ray diffraction at 1.3, 1 ligand (A24), 5 pockets (best druggability 0.73). MolNFT v2 #11592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JR0
Type: protein
Length: 515 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.3
Source: Vibrio cholerae
Molecule: cholera toxin B subunit
UniProt: P01556
Ligands: A24
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · resolution 1.3 · 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

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