MolNFT v1 · #179499 · protein

Crystal structure of diphtheria toxin from crystals obtained at pH 7.0

7K7E: “Crystal structure of diphtheria toxin from crystals obtained at pH 7.0”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #179499 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K7E
Type: protein
Length: 1,016 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin
UniProt: Q5PY51
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin	protein	509	35% helix, 27% strand	Q5PY51
B	Diphtheria toxin	protein	507	35% helix, 27% 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	795	0.74	0.78	97	empty
2	729	0.72	0.78	83	empty
3	132	0.64	0.87	39	empty
4	107	0.43	0.78	22	empty
5	71	0.41	0.80	16	empty

Interfaces

1 interface between chains.

A–B · 3709 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7K7E · Crystal structure of diphtheria toxin from crystals obtained at pH 7.0 · 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 7K7E · PDBe 7K7E · UniProt Q5PY51

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