Research workbench
Shewanella oneidensis toxin antitoxin system toxin protein hipa bound with amppnp and mg
Analyse Shewanella oneidensis toxin antitoxin system toxin protein hipa bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PU5
- Type
- protein
- Length
- 438 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin-antitoxin system toxin hipa family
- UniProt
- Q8EIX3
- Ligands
- ANP, MG, NA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin-antitoxin system toxin hipa family | protein | 438 | 38% helix, 19% strand | Q8EIX3 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.78 | 0.85 | 52 | MG, ANP, NA |
| 2 | 278 | 0.62 | 0.80 | 32 | empty |
| 3 | 125 | 0.47 | 0.78 | 29 | empty |
| 4 | 82 | 0.41 | 0.79 | 17 | empty |
Compared structures
- 4PU5 · Shewanella oneidensis Toxin Antitoxin System Toxin Protein HipA Bound with AMPPNP and Mg · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EIX3 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase toxin hipa (Q8EIX3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8EIX3
- Elsewhere: RCSB PDB 4PU5 · PDBe 4PU5 · UniProt Q8EIX3
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