Research workbench
Erve virus viral otu domain protease in complex with mouse ISG15
Analyse Erve virus viral otu domain protease in complex with mouse ISG15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JZE
- Type
- protein
- Length
- 469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein ISG15; RNA-dependent RNA polymerase
- UniProt
- Q64339, J3RTH4
- Ligands
- AYE
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Ubiquitin-like protein ISG15 | protein | 76 | 24% helix, 37% strand | Q64339 |
| A | RNA-dependent RNA polymerase | protein | 159 | 38% helix, 28% strand | J3RTH4 |
| C | RNA-dependent RNA polymerase | protein | 158 | 39% helix, 28% strand | J3RTH4 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains B, A, D, C
- FLC · Citrate anion · additive · 4 copies · chains B, A, D, C
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 | 152 | 0.63 | 0.85 | 32 | empty |
| 2 | 158 | 0.62 | 0.85 | 31 | empty |
| 3 | 298 | 0.57 | 0.76 | 39 | empty |
| 4 | 58 | 0.47 | 0.85 | 17 | empty |
| 5 | 77 | 0.46 | 0.82 | 20 | empty |
Interfaces
4 interfaces between chains.
- D–C · 976 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 976 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 118 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5JZE · Erve virus viral OTU domain protease in complex with mouse ISG15 · the same entry in another collection · chain B against B, TM-score 1.00
- Q64339 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (Q64339) · a predicted model of the same protein · chain B 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 Q64339
- Every structure of UniProt J3RTH4
- Elsewhere: RCSB PDB 5JZE · PDBe 5JZE · UniProt Q64339 · UniProt J3RTH4
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