E3 ubiquitin-protein ligase parkin (PRKN) is a 465-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O60260.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 78.1 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 32% |
| 70 to 90 | Confident: backbone generally right | 48% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 16% |
What pLDDT means and how to read it
Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (PubMed:10888878, PubMed:10973942, PubMed:11431533, PubMed:12150907, PubMed:12628165, PubMed:15105460, PubMed:16135753, PubMed:21376232, PubMed:21532592, PubMed:22396657, PubMed:23620051, PubMed:23754282, PubMed:24660806, PubMed:24751536, PubMed:29311685, PubMed:32047033). Substrates include SYT11 and VDAC1 (PubMed:29311685, PubMed:32047033). Other substrates are BCL2, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPTIN5, TOMM20, USP30, ZNF746, MIRO1 and AIMP2 (PubMed:10888878, PubMed:10973942, PubMed:11431533, PubMed:12150907,…
Forms an E3 ubiquitin ligase complex with UBE2L3 or UBE2L6 (PubMed:11078524, PubMed:21532592). Mediates 'Lys-63'-linked polyubiquitination by associating with UBE2V1. Part of a SCF-like complex, consisting of PRKN, CUL1 and FBXW7 (PubMed:12628165). Interacts with SNCAIP (PubMed:11590439, PubMed:15728840). Binds to the C2A and C2B domains of SYT11 (PubMed:12925569). Interacts and regulates the…
Cytoplasm, cytosol, Nucleus, Endoplasmic reticulum, Mitochondrion, Mitochondrion outer membrane, Cell projection, neuron projection, Postsynaptic density, Presynapse
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4I1F | X-ray | 1.58 Å | A=141-465 |
| 5C1Z | X-ray | 1.79 Å | A/B=1-465 |
| 6GLC | X-ray | 1.8 Å | A=1-382 |
| 8WZN | X-ray | 1.8 Å | A=141-465 |
| 8IKM | X-ray | 1.92 Å | A=141-382, C=1-140 |
| 4I1H | X-ray | 2.0 Å | A=141-465 |
| 4BM9 | X-ray | 2.25 Å | A=137-465 |
| 8WZO | X-ray | 2.25 Å | A=141-465 |
| 5C9V | X-ray | 2.35 Å | A=137-465 |
| 8IKV | X-ray | 2.35 Å | A/C=139-465 |
| 5C23 | X-ray | 2.37 Å | A/B=1-465 |
| 5N38 | X-ray | 2.6 Å | A=1-465 |
| 8IKT | X-ray | 2.6 Å | A=77-382, C=1-76 |
| 5N2W | X-ray | 2.68 Å | A=1-465 |
| 6HUE | X-ray | 2.85 Å | A/B=1-465 |
| 8JWV | X-ray | 2.9 Å | A=141-465 |
| 8IK6 | X-ray | 3.3 Å | A/C=139-465 |
| 1IYF | NMR | A=1-76 | |
| 2JMO | NMR | A=308-384 | |
| 5TR5 | NMR | A=1-76 |
Showing 20 of 21 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.