Ubiquitin-conjugating enzyme E2 D3 (UBE2D3) is a 147-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P61077.
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The mean pLDDT of this model is 96.4 (very high 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 | 97% |
| 70 to 90 | Confident: backbone generally right | 3% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:15247280, PubMed:15496420, PubMed:18284575, PubMed:20061386, PubMed:21532592, PubMed:28322253). In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination (PubMed:15247280, PubMed:15496420, PubMed:18284575, PubMed:20061386, PubMed:21532592). Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation (PubMed:20347421). Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin (PubMed:10329681). Ubiquitin chain…
Interacts with SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex; when Cullin is neddylated, the interaction between the E2 and the SCF complex is strengthened. Interacts with DAPK3. Interacts with BRCA1; the DNA damage checkpoint promotes the association with BRCA1 after ionizing radiation. Interacts non-covalently with ubiquitin. Interacts with E3 ubiquitin-protein ligase CBLC.…
Cell membrane, Endosome membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5EGG | X-ray | 1.76 Å | A=1-147 |
| 1X23 | X-ray | 1.85 Å | A/B/C/D=1-147 |
| 4S3O | X-ray | 2.0 Å | A/D=2-147 |
| 8UQA | X-ray | 2.05 Å | K=2-147 |
| 5IFR | X-ray | 2.2 Å | A=2-147 |
| 8UQ9 | X-ray | 2.3 Å | A/a=2-147 |
| 8UQ8 | X-ray | 2.34 Å | A/a=2-147 |
| 3UGB | X-ray | 2.35 Å | A=1-147 |
| 8AMS | X-ray | 2.4 Å | A/B=1-147 |
| 8UQB | X-ray | 2.48 Å | A=2-147 |
| 6T7F | X-ray | 2.58 Å | B=2-147 |
| 8UQC | X-ray | 2.61 Å | A=2-147 |
| 3RPG | X-ray | 2.65 Å | A=2-147 |
| 4BVU | X-ray | 2.7 Å | B=1-147 |
| 6CP0 | X-ray | 3.01 Å | B=1-147 |
| 9LPK | EM | 3.03 Å | D/E=1-147 |
| 3L1Z | X-ray | 3.17 Å | A=1-147 |
| 8SMX | EM | 3.2 Å | L=1-147 |
| 8SMY | EM | 3.2 Å | L=1-147 |
| 8SMZ | EM | 3.2 Å | L=1-147 |
Showing 20 of 45 experimental structures (best resolution first).
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