Research workbench
Toxin-antitoxin complex from Staphylococcus aureus
Analyse Toxin-antitoxin complex from Staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EWJ
- Type
- protein
- Length
- 765 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Staphylococcus aureus
- Molecule
- Endoribonuclease MazF; PemI inhibitor
- UniProt
- L7PFJ6, L7PH55
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · resolution 2 · 7 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Endoribonuclease MazF | protein | 110 | 20% helix, 35% strand | L7PFJ6 |
| B | Endoribonuclease MazF | protein | 112 | 20% helix, 34% strand | L7PFJ6 |
| C, I | PemI inhibitor | protein | 32 | 34% helix, 0% strand | L7PH55 |
| E | Endoribonuclease MazF | protein | 113 | 19% helix, 34% strand | L7PFJ6 |
| F | PemI inhibitor | protein | 31 | 32% helix, 0% strand | L7PH55 |
| G | Endoribonuclease MazF | protein | 111 | 20% helix, 34% strand | L7PFJ6 |
| H | Endoribonuclease MazF | protein | 114 | 19% helix, 33% strand | L7PFJ6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 89 | SO4 |
| 2 | 205 | 0.59 | 0.81 | 31 | empty |
| 3 | 189 | 0.55 | 0.79 | 29 | SO4 |
| 4 | 74 | 0.41 | 0.79 | 18 | empty |
| 5 | 58 | 0.35 | 0.78 | 11 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1303 Ų buried · 28 hydrogen bonds · protein-protein
- G–I · 1293 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1289 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1286 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1241 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7EWJ · Toxin-antitoxin complex from staphylococcus aureus · 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 L7PFJ6
- Every structure of UniProt L7PH55
- Elsewhere: RCSB PDB 7EWJ · PDBe 7EWJ · UniProt L7PFJ6 · UniProt L7PH55
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