Research workbench
Human josephin-2 in complex with ubiquitin
Analyse Human josephin-2 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
- 6PGV
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Josephin-2; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q8TAC2, P0CG47
- Ligands
- NEH
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Josephin-2 (EC 3.4.19.12) | protein | 152 | 36% helix, 26% strand | Q8TAC2 |
| B | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | P0CG47 |
Ligands and binding sites
- NEH · Ethanamine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.64 | 0.87 | 29 | empty |
| 2 | 102 | 0.37 | 0.75 | 18 | NEH |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, engineered).
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 Q8TAC2
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6PGV · PDBe 6PGV · UniProt Q8TAC2 · UniProt P0CG47
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