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Crystal structure of diphtheria toxin from crystals obtained at pH 5.0

Analyse Crystal structure of diphtheria toxin from crystals obtained at pH 5.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K7B
Type: protein
Length: 1,004 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin
UniProt: Q5PY51
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin	protein	504	35% helix, 27% strand	Q5PY51
B	Diphtheria toxin	protein	500	34% helix, 28% strand	Q5PY51

Pockets

10 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	734	0.72	0.78	86	empty
2	766	0.72	0.78	94	empty
3	71	0.63	0.92	30	empty
4	74	0.49	0.84	20	empty
5	81	0.49	0.83	21	empty

Interfaces

1 interface between chains.

A–B · 3546 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7K7B · Crystal structure of diphtheria toxin from crystals obtained at pH 5.0 · 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 7K7B · PDBe 7K7B · UniProt Q5PY51

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