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Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases
Analyse Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K05
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- ERI1 exoribonuclease 3
- EC
- 3.1.-.-
- UniProt
- O43414
- Ligands
- AMP, MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.85 · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ERI1 exoribonuclease 3 (EC 3.1.-.-) | protein | 200 | 39% helix, 17% strand | O43414 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.68 | 0.78 | 45 | empty |
| 2 | 206 | 0.51 | 0.76 | 24 | AMP, MG, GOL |
| 3 | 210 | 0.50 | 0.76 | 22 | AMP, MG |
Interfaces
1 interface between chains.
- A–B · 305 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7K05 · Crystal structures and ribonuclease activity of the flavivirus host factor ERI3 that is… · the same entry in another collection · chain A against A, TM-score 1.00
- O43414 · AlphaFold monomer V2.0 prediction for ERI1 exoribonuclease 3 (O43414) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O43414
- Elsewhere: RCSB PDB 7K05 · PDBe 7K05 · UniProt O43414
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