MolNFT v1 · #23070 · protein

Diphtheria toxin dimer complexed with NAD

1TOX · Diphtheria toxin (dimeric): “Diphtheria toxin dimer complexed with NAD”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.54). MolNFT v1 #23070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1TOX
Type: protein
Length: 1,028 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diphtheria toxin (dimeric)
EC: 2.4.2.36
UniProt: P00588
Ligands: NAD
Pockets: 5 · best druggability 0.54

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diphtheria toxin (dimeric) (EC 2.4.2.36)	protein	515	36% helix, 28% strand	P00588
B	Diphtheria toxin (dimeric) (EC 2.4.2.36)	protein	513	35% helix, 28% strand	P00588

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

5 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	91	0.54	0.84	23	empty
2	126	0.42	0.75	22	NAD
3	57	0.35	0.79	15	empty
4	52	0.33	0.78	13	empty
5	50	0.28	0.75	14	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1TOX · Diphtheria toxin dimer complexed with NAD · 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 1TOX · PDBe 1TOX · UniProt P00588

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