MolNFT v1 · #136364 · protein

Clostridium difficile toxin B (tcdb) glucosyltransferase domain in complex with U2F

5UQN: “Clostridium difficile toxin B (tcdb) glucosyltransferase domain in complex with U2F”. X-ray diffraction, 3 ligands (U2F, MN, SO4), 4 pockets (best druggability 0.77). MolNFT v1 #136364 on GenesisL1: 3D structure, binding sites and…

PDB: 5UQN
Type: protein
Length: 541 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin B
EC: 3.4.22.-
UniProt: P18177
Ligands: U2F, MN, SO4
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin B (EC 3.4.22.-)	protein	541	57% helix, 8% strand	P18177

Ligands and binding sites

U2F · Uridine-5'-diphosphate-2-deoxy-2-fluoro-alpha-D-glucose · ligand · chains A
MN · Manganese (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

4 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	957	0.77	0.80	92	MN, U2F, SO4
2	56	0.40	0.81	16	empty
3	51	0.37	0.80	13	empty
4	73	0.33	0.75	16	empty

Compared structures

5UQN · Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F · 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 5UQN · PDBe 5UQN · UniProt P18177

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.