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Structure of the EPSILON_1 / ZETA_1 antitoxin / toxin system from neisseria gonorrhoeae.
Analyse Structure of the EPSILON_1 / ZETA_1 antitoxin / toxin system from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EPG
- Type
- protein
- Length
- 1,792 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EPSILON_1 antitoxin; ZETA_1 toxin
- UniProt
- D5K9E3, D5K9G7
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | EPSILON_1 antitoxin | protein | 54 | 78% helix, 0% strand | D5K9E3 |
| B | ZETA_1 toxin | protein | 390 | 44% helix, 24% strand | D5K9G7 |
| C | EPSILON_1 antitoxin | protein | 56 | 70% helix, 0% strand | D5K9E3 |
| D | ZETA_1 toxin | protein | 394 | 43% helix, 24% strand | D5K9G7 |
| F | ZETA_1 toxin | protein | 395 | 43% helix, 24% strand | D5K9G7 |
| H | ZETA_1 toxin | protein | 395 | 43% helix, 24% strand | D5K9G7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.84 | 0.85 | 120 | SO4 |
| 2 | 847 | 0.81 | 0.84 | 94 | SO4 |
| 3 | 904 | 0.80 | 0.82 | 102 | SO4 |
| 4 | 1071 | 0.80 | 0.82 | 128 | SO4 |
| 5 | 83 | 0.55 | 0.86 | 19 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1910 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1891 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1878 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1866 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 544 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 modified (engineered).
Compared structures
- 6EPG · Structure of the epsilon_1 / zeta_1 antitoxin / toxin system from Neisseria gonorrhoeae. · the same entry in another collection · chain G against G, 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 D5K9E3
- Every structure of UniProt D5K9G7
- Elsewhere: RCSB PDB 6EPG · PDBe 6EPG · UniProt D5K9E3 · UniProt D5K9G7
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