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The complex of the mutated shiga toxin B subunit and GB3 trisaccharide

Analyse The complex of the mutated shiga toxin B subunit and GB3 trisaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CQF
Type: protein
Length: 345 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shiga toxin B-chain
UniProt: P08027
Ligands: BGC, GAL, GLA
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Shiga toxin B-chain	protein	69	17% helix, 48% strand	P08027

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 6 copies
GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E
GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	947	0.74	0.77	45	empty

Interfaces

5 interfaces between chains.

C–D · 669 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 660 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 651 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 650 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 649 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1CQF · The complex of the mutated shiga toxin B subunit and GB3 trisaccharide · the same entry in another collection · chain C against C, 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 P08027
Elsewhere: RCSB PDB 1CQF · PDBe 1CQF · UniProt P08027

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