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Crystal structure of peptono toxin, a diphtheria toxin homolog, from seinonella peptonophila

Analyse Crystal structure of peptono toxin, a diphtheria toxin homolog, from seinonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RB4
Type: protein
Length: 603 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin, C domain
UniProt: A0A1M4ZWA4
Ligands: IOD
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin, C domain	protein	603	33% helix, 23% strand	A0A1M4ZWA4

Ligands and binding sites

IOD · Iodide ion · ion · 26 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	226	0.77	0.91	41	IOD
2	245	0.75	0.89	36	empty
3	454	0.74	0.84	80	IOD
4	807	0.70	0.76	81	IOD
5	127	0.40	0.74	25	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7RB4 · Crystal structure of Peptono Toxin, a diphtheria toxin homolog, from Sei lla peptonophila · 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 A0A1M4ZWA4
Elsewhere: RCSB PDB 7RB4 · PDBe 7RB4 · UniProt A0A1M4ZWA4

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