Research workbench

Cholera toxin el tor B-pentamer in complex with lewis-Y

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

PDB: 5ELC
Type: protein
Length: 1,030 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholera enterotoxin subunit B
UniProt: P01556
Ligands: BCN, FUC, GAL, NDG, NAG, CA
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Cholera enterotoxin subunit B	protein	103	24% helix, 38% strand	P01556

Ligands and binding sites

BCN · Bicine · ligand · 10 copies · chains A, E, F, J, B, I, C, H, D, G
FUC · alpha-L-fucopyranose · sugar · 19 copies · chains A, E, B, C, D, F, G, H, I, J
GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, B, C, D, E, G, H, I, J
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 7 copies · chains A, B, C, E, G, H, I, J
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G
CA · Calcium ion · metal · 10 copies · chains A, F, J, B, I, C, H, D, E, G

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

Pockets

10 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	696	0.82	0.86	93	CA, BCN
2	828	0.75	0.79	43	empty
3	719	0.73	0.79	37	empty
4	254	0.70	0.86	39	CA, BCN
5	90	0.57	0.86	20	CA, BCN

Interfaces

22 interfaces between chains.

F–G · 1363 Å² buried · 30 hydrogen bonds · protein-protein
F–J · 1352 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 1329 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1327 Å² buried · 23 hydrogen bonds · protein-protein
I–J · 1321 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5ELC · Cholera toxin El Tor B-pentamer in complex with Lewis-y · the same entry in another collection · chain J against J, TM-score 1.00
P01556 · AlphaFold monomer V2.0 prediction for cholera enterotoxin subunit B (P01556) · a predicted model of the same protein · chain A 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 5ELC · PDBe 5ELC · UniProt P01556

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