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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
- 7K06
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ERI1 exoribonuclease 3
- EC
- 3.1.-.-
- UniProt
- O43414
- Ligands
- C5P, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 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
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.69 | 0.78 | 43 | empty |
| 2 | 221 | 0.51 | 0.76 | 25 | C5P |
| 3 | 200 | 0.50 | 0.76 | 24 | C5P |
| 4 | 58 | 0.36 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 310 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7K06 · 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 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 O43414
- Elsewhere: RCSB PDB 7K06 · PDBe 7K06 · UniProt O43414
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