Research workbench
Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor
Analyse Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C5C
- Type
- protein
- Length
- 690 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga-like toxin 1 B subunit
- UniProt
- P69179
- Ligands
- S10, GLA, GAL, GLC, BGC, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Shiga-like toxin 1 B subunit | protein | 69 | 16% helix, 48% strand | P69179 |
Ligands and binding sites
- S10 · Diethyl propane-1,3-diylbiscarbamate · ligand · 8 copies · chains B, D, E, G, A, J, F
- GLA · alpha-D-galactopyranose · sugar · 29 copies · chains A, B, F, J, C, G, D, E, H, I
- GAL · beta-D-galactopyranose · sugar · 12 copies · chains A, B, F, D, E, H, J
- GLC · alpha-D-glucopyranose · sugar · 10 copies · chains F, J, A, I, B, E, H
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains D, I
- SO4 · Sulfate ion · ion · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.74 | 0.77 | 45 | empty |
| 2 | 956 | 0.73 | 0.77 | 45 | empty |
| 3 | 421 | 0.57 | 0.74 | 47 | GLA, GLC, GAL, S10 |
| 4 | 107 | 0.36 | 0.73 | 13 | empty |
Interfaces
12 interfaces between chains.
- G–H · 658 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 658 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 657 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 656 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 654 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2C5C · Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor · 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 P69179
- Elsewhere: RCSB PDB 2C5C · PDBe 2C5C · UniProt P69179
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