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The refined structure of dimeric diphtheria toxin at 2.0 ångströms resolution

Analyse The refined structure of dimeric diphtheria toxin at 2.0 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DDT
Type: protein
Length: 523 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin
UniProt: P00588
Ligands: APU
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin	protein	523	36% helix, 27% strand	P00588

Ligands and binding sites

APU · Adenylyl-3'-5'-phospho-uridine-3'-monophosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	257	0.56	0.77	28	APU
2	117	0.35	0.73	24	empty
3	55	0.34	0.78	14	empty
4	50	0.27	0.74	13	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1DDT · The refined structure of dimeric diphtheria toxin at 2.0 ångströms resolution · 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 P00588
Elsewhere: RCSB PDB 1DDT · PDBe 1DDT · UniProt P00588

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