Research workbench
Crystal structure of Ebinur Lake virus cap snatching endonuclease (WT)
Analyse Crystal structure of Ebinur Lake virus cap snatching endonuclease (WT) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EWU
- Type
- protein
- Length
- 721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.11
- Source
- Abbey lake orthobunyavirus
- Molecule
- Replicase
- EC
- 2.7.7.48
- UniProt
- A0A059WLS9
- Ligands
- MN
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.11 · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase (EC 2.7.7.48) | protein | 180 | 51% helix, 13% strand | A0A059WLS9 |
| B, C | Replicase (EC 2.7.7.48) | protein | 181 | 53% helix, 13% strand | A0A059WLS9 |
| D | Replicase (EC 2.7.7.48) | protein | 179 | 53% helix, 15% strand | A0A059WLS9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.57 | 0.76 | 33 | empty |
| 2 | 171 | 0.56 | 0.80 | 29 | empty |
| 3 | 254 | 0.52 | 0.75 | 28 | empty |
| 4 | 138 | 0.42 | 0.75 | 20 | empty |
| 5 | 78 | 0.33 | 0.75 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–D · 480 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 391 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 58 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EWU · Crystal structure of ebinur lake virus cap snatching endonuclease (wt) · 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 A0A059WLS9
- Elsewhere: RCSB PDB 7EWU · PDBe 7EWU · UniProt A0A059WLS9
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