Research workbench
Crystal structure of parkin E3 ubiquitin ligase (linker deletion; delta 86-130)
Analyse Crystal structure of parkin E3 ubiquitin ligase (linker deletion; delta 86-130) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZYN
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase parkin
- EC
- 6.3.2.-
- UniProt
- Q9JK66
- Ligands
- ZN, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 367 | 20% helix, 24% strand | Q9JK66 |
| B | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 385 | 18% helix, 25% strand | Q9JK66 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.81 | 0.84 | 88 | empty |
| 2 | 70 | 0.70 | 0.95 | 22 | empty |
| 3 | 298 | 0.56 | 0.76 | 38 | empty |
| 4 | 130 | 0.55 | 0.82 | 26 | empty |
| 5 | 95 | 0.54 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4ZYN · Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JK66 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase parkin (Q9JK66) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9JK66
- Elsewhere: RCSB PDB 4ZYN · PDBe 4ZYN · UniProt Q9JK66
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