Ephrin type-B receptor 4 (EPHB4) is a 987-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P54760.
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The mean pLDDT of this model is 82.0 (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 | 46% |
| 70 to 90 | Confident: backbone generally right | 37% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 10% |
What pLDDT means and how to read it
Receptor tyrosine kinase which binds promiscuously to transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Together with its cognate ligand/functional ligand EFNB2, it is involved in the regulation of cell adhesion and migration, and plays a central role in heart morphogenesis, angiogenesis and blood vessel remodeling and permeability. EPHB4-mediated forward signaling controls cellular repulsion and segregation from…
Heterotetramer upon binding of the ligand. The heterotetramer is composed of an ephrin dimer and a receptor dimer. Oligomerization is probably required to induce biological responses (By similarity). Interacts with RASA1; the interaction depends on EPHB4 tyrosine-phosphorylation (PubMed:30578106)
Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6FNK | X-ray | 1.05 Å | A=598-892 |
| 6FNM | X-ray | 1.16 Å | A=598-892 |
| 6FNJ | X-ray | 1.24 Å | A/B=598-892 |
| 6FNL | X-ray | 1.27 Å | A=598-892 |
| 6FNI | X-ray | 1.47 Å | A=598-892 |
| 2BBA | X-ray | 1.65 Å | A=17-196 |
| 2VWX | X-ray | 1.65 Å | A=598-899 |
| 2VWY | X-ray | 1.65 Å | A=598-899 |
| 2VWZ | X-ray | 1.65 Å | A=598-899 |
| 2VX1 | X-ray | 1.65 Å | A=598-899 |
| 4BB4 | X-ray | 1.65 Å | A=598-899 |
| 2XVD | X-ray | 1.7 Å | A=598-899 |
| 2X9F | X-ray | 1.75 Å | A=598-899 |
| 2VWV | X-ray | 1.9 Å | A=598-899 |
| 2VWW | X-ray | 1.9 Å | A=598-899 |
| 2VWU | X-ray | 2.0 Å | A=598-899 |
| 2HLE | X-ray | 2.05 Å | A=17-196 |
| 2QKQ | X-ray | 2.1 Å | A/B=896-977 |
| 2VX0 | X-ray | 2.1 Å | A=598-899 |
| 2YN8 | X-ray | 2.11 Å | A/B=598-892 |
Showing 20 of 23 experimental structures (best resolution first).
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