E3 ubiquitin-protein ligase NEDD4 (NEDD4) is a 1319-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P46934.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 53.3 (low 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 | 12% |
| 70 to 90 | Confident: backbone generally right | 23% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 57% |
What pLDDT means and how to read it
E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Specifically ubiquitinates 'Lys-63' in target proteins (PubMed:19920177, PubMed:21399620, PubMed:23644597). Involved in the pathway leading to the degradation of VEGFR-2/KDFR, independently of its ubiquitin-ligase activity. Monoubiquitinates IGF1R at multiple sites, thus leading to receptor internalization and degradation in lysosomes (By similarity). Ubiquitinates FGFR1, leading to receptor internalization and degradation in lysosomes (PubMed:21765395). Promotes ubiquitination of RAPGEF2 (PubMed:11598133).…
Binds, in vitro, through the WW2 and WW3 domains, to neural isoforms of ENAH that contain the PPSY motif. Interacts with BEAN1, LITAF, RNF11, WBP1, WBP2, PMEPAI and PRRG2 (By similarity). Interacts with NDFIP1 and NDFIP2; this interaction activates the E3 ubiquitin-protein ligase and may induce its recruitment to exosomes (By similarity). Interacts with UBE2D2 (By similarity). Interaction with…
Cytoplasm, Nucleus, Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4N7F | X-ray | 1.1 Å | A/B=841-874 |
| 4N7H | X-ray | 1.7 Å | A=840-872 |
| 3B7Y | X-ray | 1.8 Å | A/B=517-571 |
| 9H9O | X-ray | 2.12 Å | A=938-1312 |
| 9H9T | X-ray | 2.17 Å | A=938-1312 |
| 5C91 | X-ray | 2.44 Å | A=938-1312 |
| 2XBF | X-ray | 2.5 Å | A=938-1319 |
| 4BBN | X-ray | 2.51 Å | A=938-1319 |
| 2XBB | X-ray | 2.68 Å | A/B=938-1319 |
| 4BE8 | X-ray | 3.0 Å | A=938-1319 |
| 5C7J | X-ray | 3.0 Å | A/B=939-1319 |
| 2KPZ | NMR | A=834-878 | |
| 2KQ0 | NMR | A=834-878 | |
| 2M3O | NMR | W=838-877 | |
| 5AHT | NMR | A=838-877 |
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.