MolNFT v1 · #117877 · protein

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

5ELE · Cholera enterotoxin subunit B: “Cholera toxin el tor B-pentamer in complex with a lewis-Y”. X-ray diffraction, 7 ligands (BCN, FUC, NDG), 9 pockets (best druggability 0.79). MolNFT v1 #117877 on GenesisL1: 3D structure, binding…

PDB: 5ELE
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, NDG, GAL, A2G, NAG, CA
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 36% 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	22% helix, 36% 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 · 10 copies · chains D, C, G, F, J, I, A, E, H
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains D, G, J
GAL · beta-D-galactopyranose · sugar · 3 copies · chains D, G, J
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 3 copies · chains D, G, J
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains F, G
CA · Calcium ion · metal · 10 copies · chains A, F, E, B, I, J, C, D, H, G
1PE · Pentaethylene glycol · additive · chains F, J

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

Pockets

9 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	676	0.79	0.84	85	CA, BCN
2	823	0.75	0.79	41	empty
3	1031	0.74	0.77	42	empty
4	280	0.70	0.85	42	CA, BCN
5	308	0.69	0.83	37	CA, BCN

Interfaces

22 interfaces between chains.

D–E · 1322 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1319 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1318 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 1316 Å² buried · 27 hydrogen bonds · protein-protein
F–J · 1304 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5ELE · Cholera toxin El Tor B-pentamer in complex with A 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 B 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 5ELE · PDBe 5ELE · UniProt P01556

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