Research workbench
Crystal structure of parkin
Analyse Crystal structure of parkin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K95
- Type
- protein
- Length
- 4,500 residues
- Chains
- 12
- 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
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 375 | 19% helix, 24% strand | Q9JK66 |
Ligands and binding sites
- ZN · Zinc ion · metal · 96 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.84 | 0.86 | 104 | empty |
| 2 | 960 | 0.84 | 0.86 | 100 | empty |
| 3 | 970 | 0.84 | 0.85 | 98 | empty |
| 4 | 903 | 0.83 | 0.85 | 98 | empty |
| 5 | 132 | 0.78 | 0.96 | 30 | empty |
Interfaces
27 interfaces between chains.
- B–D · 871 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 817 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 793 Ų buried · 11 hydrogen bonds · protein-protein
- D–I · 792 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 780 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4K95 · Crystal Structure of Parkin · the same entry in another collection · chain K against K, 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 Q9JK66
- Elsewhere: RCSB PDB 4K95 · PDBe 4K95 · UniProt Q9JK66
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