Research workbench
Ubiquitin variant bound to USP2
Analyse Ubiquitin variant bound to USP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DGF
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 2; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- O75604, P0CG47
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.4.19.12) | protein | 330 | 30% helix, 31% strand | O75604 |
| B | Polyubiquitin-B | protein | 76 | 24% helix, 33% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.59 | 0.80 | 29 | empty |
| 2 | 59 | 0.41 | 0.81 | 20 | empty |
| 3 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1828 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
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 O75604
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6DGF · PDBe 6DGF · UniProt O75604 · UniProt P0CG47
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