Research workbench
X-ray structure of turnip yellow mosaic virus PRO/DUB in complex with ubiquitin
Analyse X-ray structure of turnip yellow mosaic virus PRO/DUB in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YPT
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA replicase polyprotein; Polyubiquitin-C
- EC
- 2.1.1.-, 3.4.22.-, 3.6.4.-, 2.7.7.48
- UniProt
- P10358, P0CG48
- Ligands
- GVE
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA replicase polyprotein (EC 2.1.1.-, 3.4.22.-, 3.6.4.-, 2.7.7.48) | protein | 145 | 32% helix, 23% strand | P10358 |
| B, D | Polyubiquitin-C | protein | 75 | 23% helix, 33% strand | P0CG48 |
Ligands and binding sites
- GVE · Methyl 4-aminobutanoate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.55 | 0.77 | 27 | empty |
| 2 | 227 | 0.53 | 0.77 | 28 | empty |
| 3 | 139 | 0.50 | 0.79 | 28 | empty |
| 4 | 77 | 0.37 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 935 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 916 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 149 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6YPT · X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with 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 P10358
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6YPT · PDBe 6YPT · UniProt P10358 · UniProt P0CG48
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