Low-density lipoprotein receptor (LDLR) is a 860-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P01130.
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The mean pLDDT of this model is 75.4 (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 | 28% |
| 70 to 90 | Confident: backbone generally right | 45% |
| 50 to 70 | Low: treat with caution | 11% |
| Below 50 | Very low: often disordered regions | 17% |
What pLDDT means and how to read it
Binds low density lipoprotein /LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Forms a ternary complex with PGRMC1 and TMEM97 receptors which increases LDLR-mediated LDL internalization (PubMed:30443021)
Interacts (via NPXY motif) with DAB2 (via PID domain); the interaction is impaired by tyrosine phosphorylation of the NPXY motif (By similarity). Interacts (via NPXY motif) with LDLRAP1 (via PID domain) (PubMed:12221107, PubMed:22509010). Interacts with ARRB1 (PubMed:12944399). Interacts with SNX17 (PubMed:14739284). Interacts with the full-length immature form of PCSK9 (via C-terminus)…
Cell membrane, Membrane, clathrin-coated pit, Golgi apparatus, Early endosome, Late endosome, Lysosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2FCW | X-ray | 1.26 Å | B=107-186 |
| 3SO6 | X-ray | 1.37 Å | Q=819-832 |
| 1IJQ | X-ray | 1.5 Å | A/B=398-713 |
| 1AJJ | X-ray | 1.7 Å | A=196-232 |
| 5OYL | X-ray | 2.25 Å | D=65-106 |
| 2W2N | X-ray | 2.3 Å | E=314-393 |
| 2W2Q | X-ray | 2.33 Å | E=314-393 |
| 2W2M | X-ray | 2.4 Å | E=314-393 |
| 3BPS | X-ray | 2.41 Å | E=314-393 |
| 4NE9 | X-ray | 2.6 Å | D=314-339 |
| 2W2O | X-ray | 2.62 Å | E=314-393 |
| 2W2P | X-ray | 2.62 Å | E=314-393 |
| 3GCW | X-ray | 2.7 Å | E=314-393 |
| 3GCX | X-ray | 2.7 Å | E=314-393 |
| 3P5B | X-ray | 3.3 Å | L=316-715 |
| 5OY9 | X-ray | 3.6 Å | D=108-144 |
| 1N7D | X-ray | 3.7 Å | A=22-720 |
| 9COO | EM | 3.73 Å | R=66-860 |
| 9BDE | EM | 4.18 Å | R=1-860 |
| 3P5C | X-ray | 4.2 Å | L=276-715 |
Showing 20 of 36 experimental structures (best resolution first).
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