MolNFT v1 · #32610 · protein

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

2BVM: “Crystal structure of the catalytic domain of toxin B from clostridium difficile in complex with udp, glc and…”. X-ray diffraction, 4 ligands (UDP, GLC, MN), 3 pockets (best druggability 0.74). MolNFT v1 #32610 on GenesisL1: 3D…

PDB: 2BVM
Type: protein
Length: 541 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: UDP, GLC, MN, SO4
Pockets: 3 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin B (EC 2.4.1.-)	protein	541	57% helix, 8% strand	P18177

Ligands and binding sites

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

3 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	626	0.74	0.80	58	MN, UDP, GLC, SO4
2	186	0.49	0.77	26	empty
3	50	0.36	0.79	11	empty

Compared structures

2BVM · 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 2BVM · PDBe 2BVM · UniProt P18177

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