Research workbench
SHIGA TOXIN
Analyse SHIGA TOXIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DM0
- Type
- protein
- Length
- 1,216 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga toxin a subunit; Shiga toxin B subunit
- EC
- 3.2.2.22
- UniProt
- Q7BQ99, Q7BQ98
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shiga toxin a subunit (EC 3.2.2.22) | protein | 264 | 38% helix, 25% strand | Q7BQ99 |
| L | Shiga toxin a subunit (EC 3.2.2.22) | protein | 262 | 37% helix, 22% strand | Q7BQ99 |
| B, C, D, E, F, G, H, I, J, K | Shiga toxin B subunit | protein | 69 | 17% helix, 36% strand | Q7BQ98 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.76 | 0.84 | 54 | empty |
| 2 | 374 | 0.73 | 0.84 | 42 | empty |
| 3 | 688 | 0.70 | 0.77 | 55 | empty |
| 4 | 635 | 0.68 | 0.77 | 68 | empty |
| 5 | 182 | 0.47 | 0.75 | 29 | empty |
Interfaces
34 interfaces between chains.
- B–F · 680 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 665 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 651 Ų buried · 12 hydrogen bonds · protein-protein
- G–K · 636 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1DM0 · SHIGA TOXIN · the same entry in another collection · chain K against K, 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 Q7BQ99
- Every structure of UniProt Q7BQ98
- Elsewhere: RCSB PDB 1DM0 · PDBe 1DM0 · UniProt Q7BQ99 · UniProt Q7BQ98
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