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Cholera holotoxin, crystal form 1

Analyse Cholera holotoxin, crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S5E
Type: protein
Length: 1,488 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cholera enterotoxin, a chain precursor; Cholera toxin B protein (ctb)
EC: 2.4.2.36
UniProt: P01555, P01556
Ligands: GAL, NA
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cholera enterotoxin, a chain precursor (EC 2.4.2.36)	protein	232	38% helix, 18% strand	P01555
D, E, F, H, J, K, L, M, N	Cholera toxin B protein (ctb)	protein	103	23% helix, 37% strand	P01556
G	Cholera toxin B protein (ctb)	protein	102	25% helix, 38% strand	P01556
B	Cholera enterotoxin, a chain precursor (EC 2.4.2.36)	protein	227	38% helix, 19% strand	P01555

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 2 copies · chains D, J
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.80	0.90	46	empty
2	746	0.78	0.82	74	empty
3	267	0.69	0.85	39	empty
4	320	0.69	0.83	37	empty
5	214	0.59	0.81	30	empty

Interfaces

22 interfaces between chains.

E–F · 1356 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 1351 Å² buried · 22 hydrogen bonds · protein-protein
J–K · 1294 Å² buried · 23 hydrogen bonds · protein-protein
F–G · 1293 Å² buried · 23 hydrogen bonds · protein-protein
J–N · 1277 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1S5E · Cholera holotoxin, Crystal form 1 · the same entry in another collection · chain N against N, 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 P01555
Every structure of UniProt P01556
Elsewhere: RCSB PDB 1S5E · PDBe 1S5E · UniProt P01555 · UniProt P01556

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