MolNFT v1 · #179498 · protein

Crystal structure of diphtheria toxin from crystals obtained at pH 6.0

7K7D: “Crystal structure of diphtheria toxin from crystals obtained at pH 6.0”. X-ray diffraction, 9 pockets (best druggability 0.75). MolNFT v1 #179498 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K7D
Type: protein
Length: 1,012 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin
UniProt: Q5PY51
Pockets: 9 · best druggability 0.75

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin	protein	507	35% helix, 28% strand	Q5PY51
B	Diphtheria toxin	protein	505	35% helix, 28% strand	Q5PY51

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.75	0.80	98	empty
2	697	0.71	0.78	82	empty
3	90	0.42	0.79	16	empty
4	132	0.40	0.74	29	empty
5	69	0.40	0.80	17	empty

Interfaces

1 interface between chains.

A–B · 3570 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7K7D · Crystal structure of diphtheria toxin from crystals obtained at pH 6.0 · 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 7K7D · PDBe 7K7D · UniProt Q5PY51

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