Research workbench
The refined structure of monomeric diphtheria toxin at 2.3 ångströms resolution
Analyse The refined structure of monomeric diphtheria toxin at 2.3 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MDT
- Type
- protein
- Length
- 1,046 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphtheria toxin
- UniProt
- P00588
- Ligands
- APU
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diphtheria toxin | protein | 523 | 34% helix, 28% strand | P00588 |
Ligands and binding sites
- APU · Adenylyl-3'-5'-phospho-uridine-3'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.75 | 0.80 | 88 | APU |
| 2 | 707 | 0.75 | 0.80 | 76 | APU |
| 3 | 101 | 0.43 | 0.78 | 25 | empty |
| 4 | 80 | 0.40 | 0.78 | 22 | empty |
| 5 | 134 | 0.39 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 398 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MDT · The refined structure of monomeric diphtheria toxin at 2.3 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 1MDT · PDBe 1MDT · UniProt P00588
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