Research workbench
1.55 ångström crystal structure of wild type diphtheria toxin
Analyse 1.55 ångström crystal structure of wild type diphtheria toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F0L
- Type
- protein
- Length
- 1,042 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphtheria toxin
- UniProt
- P00588
- Ligands
- APU, CL
- Pockets
- 11 · 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 | 520 | 35% helix, 28% strand | P00588 |
| B | Diphtheria toxin | protein | 522 | 35% helix, 28% strand | P00588 |
Ligands and binding sites
- APU · Adenylyl-3'-5'-phospho-uridine-3'-monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.75 | 0.80 | 81 | CL, APU |
| 2 | 750 | 0.75 | 0.80 | 81 | CL, APU |
| 3 | 174 | 0.44 | 0.74 | 40 | empty |
| 4 | 56 | 0.42 | 0.82 | 17 | empty |
| 5 | 90 | 0.35 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1F0L · 1.55 ångström crystal structure of wild type diphtheria toxin · 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 1F0L · PDBe 1F0L · UniProt P00588
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