Research workbench
Rebuilt and re-refined pdb entry 5YEP: tri-ampylated shewanella oneidensis hepn toxin in complex with mnt antitoxin
Analyse Rebuilt and re-refined pdb entry 5YEP: tri-ampylated shewanella oneidensis hepn… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AER
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin-antitoxin system antidote mnt family; Toxin-antitoxin system toxin hepn family
- UniProt
- Q8ECH7, Q8ECH6
- Ligands
- AMP
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin-antitoxin system antidote mnt family | protein | 119 | 56% helix, 21% strand | Q8ECH7 |
| B | Toxin-antitoxin system toxin hepn family | protein | 133 | 77% helix, 0% strand | Q8ECH6 |
| C, D | Toxin-antitoxin system toxin hepn family | protein | 132 | 77% helix, 0% strand | Q8ECH6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 6 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.70 | 0.79 | 57 | empty |
| 2 | 249 | 0.56 | 0.78 | 44 | AMP |
| 3 | 209 | 0.53 | 0.77 | 31 | empty |
| 4 | 155 | 0.52 | 0.79 | 24 | empty |
| 5 | 131 | 0.46 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 877 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 170 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 7AER · Rebuilt and re-refined PDB entry 5yep: tri-AMPylated Shewanella oneidensis HEPN toxin in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ECH6 · AlphaFold monomer V2.0 prediction for mRNA nuclease hept (Q8ECH6) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q8ECH7 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase mnta (Q8ECH7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8ECH7
- Every structure of UniProt Q8ECH6
- Elsewhere: RCSB PDB 7AER · PDBe 7AER · UniProt Q8ECH7 · UniProt Q8ECH6
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