Research workbench

Crystal structure of diphtheria toxin from crystals obtained at pH 5.5

Analyse Crystal structure of diphtheria toxin from crystals obtained at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K7C
Type: protein
Length: 1,002 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin
UniProt: Q5PY51
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin	protein	502	34% helix, 28% strand	Q5PY51
B	Diphtheria toxin	protein	500	34% helix, 28% strand	Q5PY51

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	744	0.72	0.78	86	empty
2	682	0.70	0.78	83	empty
3	269	0.63	0.81	55	empty
4	74	0.48	0.83	21	empty
5	85	0.45	0.81	20	empty

Interfaces

1 interface between chains.

A–B · 3497 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7K7C · Crystal structure of diphtheria toxin from crystals obtained at pH 5.5 · 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 Q5PY51
Elsewhere: RCSB PDB 7K7C · PDBe 7K7C · UniProt Q5PY51

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