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Crystal structure of the catalytic domain of toxin B from clostridium difficile in complex with udp, glc and manganese ion

Analyse Crystal structure of the catalytic domain of toxin B from clostridium difficile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BVL
Type: protein
Length: 543 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin B
EC: 2.4.1.-
UniProt: P18177
Ligands: TBR, UDP, GLC, MN, SO4
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 59% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin B (EC 2.4.1.-)	protein	543	59% helix, 8% strand	P18177

Ligands and binding sites

TBR · Hexatantalum dodecabromide · ligand · 4 copies · chains A
UDP · Uridine-5'-diphosphate · ligand · chains A
GLC · alpha-D-glucopyranose · sugar · chains A
MN · Manganese (II) ion · metal · chains A
SO4 · Sulfate ion · ion · chains A

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	872	0.75	0.79	90	MN, UDP, GLC

Compared structures

2BVL · Crystal structure of the catalytic domain of toxin B from Clostridium difficile in… · the same entry in another collection · chain A against A, 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 P18177
Elsewhere: RCSB PDB 2BVL · PDBe 2BVL · UniProt P18177

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