Neuropilin-1 (NRP1) is a 923-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O14786.
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The mean pLDDT of this model is 79.1 (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 | 45% |
| 70 to 90 | Confident: backbone generally right | 32% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 17% |
What pLDDT means and how to read it
Cell-surface receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. Mediates the chemorepulsant activity of semaphorins (PubMed:10688880, PubMed:9288753, PubMed:9529250). Recognizes a C-end rule (CendR) motif R/KXXR/K on its ligands which causes cellular internalization and vascular leakage (PubMed:19805273). It binds to semaphorin 3A, the PLGF-2 isoform of PGF, the VEGF165 isoform of VEGFA and VEGFB (PubMed:10688880, PubMed:19805273, PubMed:9288753, PubMed:9529250). Coexpression with KDR results in increased VEGF165 binding to KDR as well as increased chemotaxis.…
Homodimer, and heterodimer with NRP2 (PubMed:17989695). Interacts with FER (By similarity). Interacts with PLXNB1 (PubMed:10520995). Interacts with VEGFA (PubMed:19805273, PubMed:26503042). Interacts with ABCB8/MITOSUR in mitochondria (PubMed:30623799)
Secreted, Mitochondrion membrane, Cell membrane, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6FMC | X-ray | 0.9 Å | A=273-427 |
| 6TKK | X-ray | 1.06 Å | A=273-427 |
| 8PFE | X-ray | 1.35 Å | A/C=273-427 |
| 5JGI | X-ray | 1.38 Å | A/B=273-427 |
| 5C7G | X-ray | 1.45 Å | A=273-427 |
| 5IJR | X-ray | 1.52 Å | A/B=273-427 |
| 9EOU | X-ray | 1.55 Å | A=273-586 |
| 7O1N | X-ray | 1.56 Å | A=273-427 |
| 9F6B | X-ray | 1.57 Å | A/B=273-427 |
| 5IYY | X-ray | 1.6 Å | A/B=273-427 |
| 5JGQ | X-ray | 1.6 Å | A/B=273-427 |
| 7P5U | X-ray | 1.6 Å | AAA/BBB=273-427 |
| 4RN5 | X-ray | 1.73 Å | A=273-427 |
| 2QQI | X-ray | 1.8 Å | A=273-586 |
| 5JHK | X-ray | 1.8 Å | A/B=273-427 |
| 1KEX | X-ray | 1.9 Å | A=273-427 |
| 2QQM | X-ray | 2.0 Å | A=141-586 |
| 5J1X | X-ray | 2.1 Å | A/B/C/D=273-427 |
| 2QQN | X-ray | 2.2 Å | A=273-427 |
| 5L73 | X-ray | 2.24 Å | A/B=628-813 |
Showing 20 of 25 experimental structures (best resolution first).
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