Research workbench
Structure of a viral otu domain protease bound to ubiquitin
Analyse Structure of a viral otu domain protease bound to ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PT2
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase; Ubiquitin B
- UniProt
- Q6TQF5, Q5U5U6
- Ligands
- 3CN, SO4
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase | protein | 164 | 39% helix, 25% strand | Q6TQF5 |
| B | Ubiquitin B | protein | 75 | 24% helix, 35% strand | Q5U5U6 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1024 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 3PT2 · Structure of a viral OTU domain protease bound to Ubiquitin · 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 Q6TQF5
- Every structure of UniProt Q5U5U6
- Elsewhere: RCSB PDB 3PT2 · PDBe 3PT2 · UniProt Q6TQF5 · UniProt Q5U5U6
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