Research workbench
Structure of shiga toxin type 2 (STX2) B pentamer mutant Q40L
Analyse Structure of shiga toxin type 2 (STX2) B pentamer mutant Q40L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MXG
- Type
- protein
- Length
- 700 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga-like toxin 2 subunit B
- UniProt
- A7UQX3
- Ligands
- XLS
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Shiga-like toxin 2 subunit B | protein | 70 | 14% helix, 46% strand | A7UQX3 |
Ligands and binding sites
- XLS · D-xylose · ligand · 4 copies · chains A, F, G, B, C, J, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.83 | 0.85 | 54 | empty |
| 2 | 1146 | 0.82 | 0.83 | 66 | empty |
| 3 | 226 | 0.64 | 0.83 | 20 | empty |
| 4 | 197 | 0.60 | 0.82 | 32 | XLS |
| 5 | 106 | 0.55 | 0.84 | 20 | empty |
Interfaces
22 interfaces between chains.
- I–J · 746 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 743 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 743 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 740 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 729 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3MXG · Structure of Shiga Toxin type 2 (Stx2) B Pentamer Mutant Q40L · 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 A7UQX3
- Elsewhere: RCSB PDB 3MXG · PDBe 3MXG · UniProt A7UQX3
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