Research workbench
Structure of a toxin-antitoxin system bound to its substrate
Analyse Structure of a toxin-antitoxin system bound to its substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q8X
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antidote of epsilon-zeta postsegregational killing system; Zeta-toxin
- UniProt
- Q6UZC8, Q54944
- Ligands
- UD1, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antidote of epsilon-zeta postsegregational killing system | protein | 85 | 75% helix, 0% strand | Q6UZC8 |
| B | Zeta-toxin | protein | 272 | 57% helix, 10% strand | Q54944 |
| C | Antidote of epsilon-zeta postsegregational killing system | protein | 85 | 74% helix, 0% strand | Q6UZC8 |
| D | Zeta-toxin | protein | 271 | 55% helix, 10% strand | Q54944 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.83 | 0.90 | 45 | empty |
| 2 | 419 | 0.82 | 0.89 | 38 | empty |
| 3 | 926 | 0.79 | 0.81 | 85 | SO4, UD1 |
| 4 | 610 | 0.75 | 0.82 | 60 | SO4 |
| 5 | 67 | 0.39 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1532 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1503 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1122 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 Q6UZC8
- Every structure of UniProt Q54944
- Elsewhere: RCSB PDB 3Q8X · PDBe 3Q8X · UniProt Q6UZC8 · UniProt Q54944
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