MolNFT v1 · #147847 · protein
Structure of the EPSILON_1 / ZETA_1 antitoxin / toxin system from neisseria gonorrhoeae in complex with unam-4P.
6EPI · EPSILON_1 antitoxin: “Structure of the EPSILON_1 / ZETA_1 antitoxin / toxin system from neisseria gonorrhoeae in complex with…”. X-ray diffraction, 2 ligands (BNW, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #147847 on…
- PDB
- 6EPI
- Type
- protein
- Length
- 1,789 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
- BNW, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | EPSILON_1 antitoxin | protein | 52 | 81% helix, 0% strand | D5K9E3 |
| B, D | ZETA_1 toxin | protein | 394 | 43% helix, 24% strand | D5K9G7 |
| C | EPSILON_1 antitoxin | protein | 54 | 76% helix, 0% strand | D5K9E3 |
| F, H | ZETA_1 toxin | protein | 395 | 43% helix, 24% strand | D5K9G7 |
| G | EPSILON_1 antitoxin | protein | 53 | 77% helix, 0% strand | D5K9E3 |
Ligands and binding sites
- BNW · UDP-N-acetyl-muramic acid-4'phosphate · ligand · 4 copies · chains B, D, F, H
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F, G, H
- FLC · Citrate anion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.81 | 0.82 | 108 | BNW, SO4 |
| 2 | 888 | 0.80 | 0.82 | 104 | BNW, SO4 |
| 3 | 568 | 0.71 | 0.80 | 56 | BNW, SO4 |
| 4 | 573 | 0.71 | 0.80 | 61 | BNW, SO4 |
| 5 | 603 | 0.70 | 0.78 | 62 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1841 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1802 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1791 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1784 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 518 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EPI · Structure of the epsilon_1 / zeta_1 antitoxin / toxin system from Neisseria gonorrhoeae… · 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 D5K9E3
- Every structure of UniProt D5K9G7
- Elsewhere: RCSB PDB 6EPI · PDBe 6EPI · UniProt D5K9E3 · UniProt D5K9G7
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