MolNFT v1 · #97220 · protein
Crystal structure of parkin C-terminal ring domains
4K7D · E3 ubiquitin-protein ligase parkin: “Crystal structure of parkin C-terminal ring domains”. X-ray diffraction, 2 ligands (ZN, CL), 17 pockets (best druggability 0.68). MolNFT v1 #97220 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K7D
- Type
- protein
- Length
- 922 residues
- Chains
- 3
- 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, CL
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 306 | 19% helix, 24% strand | Q9JK66 |
| B | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 312 | 18% helix, 24% strand | Q9JK66 |
| C | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 304 | 18% helix, 23% strand | Q9JK66 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C
- CL · Chloride ion · ion · chains C
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.68 | 0.77 | 63 | empty |
| 2 | 506 | 0.68 | 0.78 | 52 | empty |
| 3 | 51 | 0.44 | 0.84 | 16 | empty |
| 4 | 155 | 0.42 | 0.74 | 29 | empty |
| 5 | 105 | 0.41 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 939 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 446 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 5 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 Q9JK66
- Elsewhere: RCSB PDB 4K7D · PDBe 4K7D · UniProt Q9JK66
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.