Research workbench
Crystal structure of di-ampylated HEPN(R102A) toxin
Analyse Crystal structure of di-ampylated HEPN(R102A) toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AE6
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepn toxin
- UniProt
- A0A0B0QJR1
- Ligands
- AMP
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepn toxin | protein | 147 | 80% helix, 0% strand | A0A0B0QJR1 |
| B | Hepn toxin | protein | 143 | 78% helix, 0% strand | A0A0B0QJR1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.55 | 0.79 | 22 | empty |
| 2 | 161 | 0.46 | 0.76 | 26 | empty |
| 3 | 113 | 0.46 | 0.79 | 20 | AMP, EDO |
| 4 | 119 | 0.43 | 0.77 | 21 | AMP, EDO |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7AE6 · Crystal structure of di-AMPylated HEPN(R102A) toxin · 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 A0A0B0QJR1
- Elsewhere: RCSB PDB 7AE6 · PDBe 7AE6 · UniProt A0A0B0QJR1
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