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Heat-labile enterotoxin B-pentamer complexed with para-aminophenyl- alpha-D-galactopyranoside

Analyse Heat-labile enterotoxin B-pentamer complexed with para-aminophenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EFI
Type: protein
Length: 515 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (heat-labile enterotoxin B chain)
UniProt: P32890
Ligands: GAT
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F, G, H	Protein (heat-labile enterotoxin B chain)	protein	103	22% helix, 37% strand	P32890

Ligands and binding sites

GAT · 4-aminophenyl alpha-D-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	1103	0.74	0.77	58	empty
2	79	0.42	0.79	18	empty
3	55	0.36	0.79	18	empty
4	68	0.33	0.75	14	GAT
5	52	0.29	0.75	13	GAT

Interfaces

5 interfaces between chains.

F–G · 1374 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1364 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 1360 Å² buried · 31 hydrogen bonds · protein-protein
D–H · 1345 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1327 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1EFI · Heat-labile enterotoxin B-pentamer complexed with… · the same entry in another collection · chain H against H, TM-score 1.00
P32890 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin B chain (P32890) · a predicted model of the same protein · chain E 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 P32890
Elsewhere: RCSB PDB 1EFI · PDBe 1EFI · UniProt P32890

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