MolNFT v1 · #105275 · protein

Clostridium difficile toxin a (tcda)

4R04: “Clostridium difficile toxin a (tcda)”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #105275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4R04
Type: protein
Length: 1,793 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin a
UniProt: P16154
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin a	protein	1793	35% helix, 23% strand	P16154

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	776	0.86	0.89	100	empty
2	777	0.85	0.88	84	empty
3	430	0.74	0.84	45	empty
4	50	0.72	0.98	13	empty
5	164	0.72	0.90	33	empty

Compared structures

4R04 · Clostridium difficile Toxin A (TcdA) · 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 P16154
Elsewhere: RCSB PDB 4R04 · PDBe 4R04 · UniProt P16154

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