MolNFT v1 · #94459 · protein
Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases
4HXD · Polyubiquitin-C: “Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases”. X-ray diffraction, 2 ligands (3CN, SO4), 7 pockets (best druggability 0.66). MolNFT v1 #94459 on GenesisL1…
- 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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