Research workbench
Structure of the pseudomonas putida res-xre toxin-antitoxin complex
Analyse Structure of the pseudomonas putida res-xre toxin-antitoxin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GW6
- Type
- protein
- Length
- 886 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Res toxin; Xre antitoxin
- UniProt
- A0A179RGC3, A0A179RFM7
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Res toxin | protein | 145 | 28% helix, 25% strand | A0A179RGC3 |
| B, C, E, F | Xre antitoxin | protein | 149 | 70% helix, 1% strand | A0A179RFM7 |
Ligands and binding sites
- IMD · Imidazole · additive · 2 copies · chains A, B, D, E
- GOL · Glycerol · additive · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.80 | 0.82 | 123 | IMD |
| 2 | 379 | 0.78 | 0.87 | 59 | empty |
| 3 | 404 | 0.72 | 0.83 | 55 | empty |
| 4 | 82 | 0.52 | 0.85 | 16 | empty |
| 5 | 102 | 0.48 | 0.81 | 15 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1454 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1429 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1245 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1171 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1159 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6GW6 · Structure of the Pseudomonas putida RES-Xre toxin-antitoxin complex · 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 A0A179RGC3
- Every structure of UniProt A0A179RFM7
- Elsewhere: RCSB PDB 6GW6 · PDBe 6GW6 · UniProt A0A179RGC3 · UniProt A0A179RFM7
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