Research workbench
The crystal structure of STX2 and a disaccharide ligand
Analyse The crystal structure of STX2 and a disaccharide ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M1U
- Type
- protein
- Length
- 631 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga toxin 2 a-subunit; Shiga toxin 2 B subunit
- EC
- 3.2.2.22
- UniProt
- Q7DI68, Q7DJJ2
- Ligands
- 1PS, MBG, A2G
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shiga toxin 2 a-subunit (EC 3.2.2.22) | protein | 281 | 38% helix, 24% strand | Q7DI68 |
| B, C, D, E, F | Shiga toxin 2 B subunit | protein | 70 | 16% helix, 47% strand | Q7DJJ2 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 3 copies · chains B, C, D
- MBG · methyl beta-D-galactopyranoside · ligand · 2 copies · chains F, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains E, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.71 | 0.78 | 53 | empty |
| 2 | 189 | 0.47 | 0.76 | 35 | empty |
Interfaces
10 interfaces between chains.
- E–F · 759 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 750 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 742 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 735 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 693 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4M1U · The crystal structure of Stx2 and a disaccharide ligand · 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 Q7DI68
- Every structure of UniProt Q7DJJ2
- Elsewhere: RCSB PDB 4M1U · PDBe 4M1U · UniProt Q7DI68 · UniProt Q7DJJ2
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