MolNFT v1 · #150157 · protein
Structure of phospho-parkin bound to phospho-ubiquitin
6GLC · E3 ubiquitin-protein ligase parkin: “Structure of phospho-parkin bound to phospho-ubiquitin”. X-ray diffraction, 3 ligands (3CN, ZN, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #150157 on GenesisL1: 3D structure, binding…
- PDB
- 6GLC
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase parkin; Polyubiquitin-B
- EC
- 2.3.2.31
- UniProt
- O60260, P0CG47
- Ligands
- 3CN, ZN, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase parkin (EC 2.3.2.31) | protein | 316 | 20% helix, 28% strand | O60260 |
| B | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
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 | 519 | 0.73 | 0.81 | 55 | MPD |
| 2 | 124 | 0.40 | 0.75 | 22 | empty |
| 3 | 93 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1441 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 6GLC · Structure of phospho-Parkin bound to phospho-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- O60260 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase parkin (O60260) · a predicted model of the same protein · chain A against A, TM-score 0.59
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 O60260
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6GLC · PDBe 6GLC · UniProt O60260 · UniProt P0CG47
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