Research workbench
Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. COLI
Analyse Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XSC
- Type
- protein
- Length
- 345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga-like toxin 1 subunit B
- UniProt
- P69178
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Shiga-like toxin 1 subunit B | protein | 69 | 19% helix, 48% strand | P69178 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.78 | 0.82 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–E · 697 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 677 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 668 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2XSC · Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli · 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 P69178
- Elsewhere: RCSB PDB 2XSC · PDBe 2XSC · UniProt P69178
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.