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Cholera toxin classical B-pentamer in complex with fucose

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

PDB: 6HMW
Type: protein
Length: 1,029 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholera enterotoxin B-subunit
UniProt: Q57193
Ligands: BCN, FUL, CA
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H, I, J	Cholera enterotoxin B-subunit	protein	103	23% helix, 37% strand	Q57193
G	Cholera enterotoxin B-subunit	protein	102	25% helix, 35% strand	Q57193

Ligands and binding sites

BCN · Bicine · ligand · 10 copies · chains A, E, I, J, B, H, C, G, D, F
FUL · beta-L-fucopyranose · sugar · 16 copies · chains A, E, B, C, D, F, G, J, H, I
CA · Calcium ion · metal · 10 copies · chains A, I, J, E, B, H, C, D, F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.81	0.82	96	CA, BCN
2	977	0.77	0.79	44	empty
3	886	0.76	0.79	42	empty
4	336	0.68	0.82	37	BCN, CA
5	211	0.62	0.82	25	CA, BCN

Interfaces

23 interfaces between chains.

F–J · 1352 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1339 Å² buried · 24 hydrogen bonds · protein-protein
H–I · 1318 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 1311 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 1308 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, glycosylation).

Compared structures

6HMW · Cholera toxin classical B-pentamer in complex with fucose · the same entry in another collection · chain A 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 Q57193
Elsewhere: RCSB PDB 6HMW · PDBe 6HMW · UniProt Q57193

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