Research workbench
Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases
Analyse Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HXD
- Type
- protein
- Length
- 463 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C; RNA-directed RNA polymerase L
- EC
- 3.4.19.12, 2.7.7.48
- UniProt
- P0CG48, Q66431
- Ligands
- 3CN, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyubiquitin-C (EC 3.4.19.12) | protein | 75 | 24% helix, 35% strand | P0CG48 |
| B | RNA-directed RNA polymerase L (EC 3.4.19.12, 2.7.7.48) | protein | 157 | 37% helix, 25% strand | Q66431 |
| D | RNA-directed RNA polymerase L (EC 3.4.19.12, 2.7.7.48) | protein | 156 | 37% helix, 27% strand | Q66431 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.66 | 0.80 | 34 | empty |
| 2 | 155 | 0.48 | 0.77 | 29 | empty |
| 3 | 90 | 0.43 | 0.79 | 17 | empty |
| 4 | 65 | 0.41 | 0.80 | 15 | empty |
| 5 | 65 | 0.39 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1031 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4HXD · Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor… · 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 P0CG48
- Every structure of UniProt Q66431
- Elsewhere: RCSB PDB 4HXD · PDBe 4HXD · UniProt P0CG48 · UniProt Q66431
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