Beta-secretase 1 (BACE1) is a 501-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P56817.
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The mean pLDDT of this model is 87.5 (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 | 74% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 11% |
What pLDDT means and how to read it
Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase (PubMed:10656250, PubMed:10677483, PubMed:20354142). Cleaves CHL1 (By similarity)
Monomer. Interacts (via DXXLL motif) with GGA1, GGA2 and GGA3 (via their VHS domain); the interaction highly increases when BACE1 is phosphorylated at Ser-498 (PubMed:14567678, PubMed:15886016). Interacts with RTN1; RTN2; RTN3 and RTN4; the interaction leads to inhibition of amyloid precursor protein processing (PubMed:15286784, PubMed:16965550, PubMed:16979658). Interacts with SNX6…
Cell membrane, Golgi apparatus, trans-Golgi network, Endoplasmic reticulum, Endosome, Cell surface, Cytoplasmic vesicle membrane, Membrane raft, Lysosome, Late endosome, Early endosome, Recycling endosome, Cell projection, axon, Cell projection, dendrite
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7MYI | X-ray | 1.25 Å | A/B=14-454 |
| 6UWP | X-ray | 1.29 Å | A/B=14-454 |
| 6EQM | X-ray | 1.35 Å | A=48-447 |
| 4L7G | X-ray | 1.38 Å | A=57-453 |
| 6EJ2 | X-ray | 1.46 Å | A=1-501 |
| 6UWV | X-ray | 1.47 Å | A/B=14-454 |
| 3VF3 | X-ray | 1.48 Å | A=48-447 |
| 5HDZ | X-ray | 1.49 Å | A/B=41-454 |
| 2QP8 | X-ray | 1.5 Å | A/B=55-447 |
| 4B78 | X-ray | 1.5 Å | A=62-445 |
| 4DJX | X-ray | 1.5 Å | A/B=41-454 |
| 5HU1 | X-ray | 1.5 Å | A/B=43-454 |
| 6BFE | X-ray | 1.51 Å | A/B=14-454 |
| 3VEU | X-ray | 1.52 Å | A=48-447 |
| 5F01 | X-ray | 1.52 Å | A=57-446 |
| 3L5E | X-ray | 1.53 Å | A/B=41-454 |
| 5HE4 | X-ray | 1.53 Å | A/B=41-454 |
| 6FGY | X-ray | 1.54 Å | A=60-453 |
| 5HE5 | X-ray | 1.55 Å | A/B=41-454 |
| 4FM7 | X-ray | 1.56 Å | A=58-453 |
Showing 20 of 431 experimental structures (best resolution first).
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