Ephrin-B2 (EFNB2) is a 333-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P52799.
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The mean pLDDT of this model is 70.8 (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 | 36% |
| 70 to 90 | Confident: backbone generally right | 17% |
| 50 to 70 | Low: treat with caution | 15% |
| Below 50 | Very low: often disordered regions | 32% |
What pLDDT means and how to read it
Cell surface transmembrane ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors 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. Binds to receptor tyrosine kinase including EPHA4, EPHA3 and EPHB4. Together with EPHB4 plays a central role in heart morphogenesis and angiogenesis through regulation of cell…
Interacts with PDZRN3 (By similarity). Binds to the receptor tyrosine kinases EPHA4, EPHB4 and EPHA3
Cell membrane, Cell junction, adherens junction
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4UF7 | X-ray | 1.7 Å | C/E=27-167 |
| 2VSM | X-ray | 1.8 Å | B=28-166 |
| 2HLE | X-ray | 2.05 Å | B=28-165 |
| 2WO2 | X-ray | 2.45 Å | B=27-167 |
| 3GXU | X-ray | 2.5 Å | B=27-169 |
| 6PDL | X-ray | 2.7 Å | B/D/F/H=27-167 |
| 6P7Y | X-ray | 2.84 Å | B/D=27-170 |
| 9DVD | EM | 2.9 Å | B=27-164 |
| 2VSK | X-ray | 3.3 Å | B/D=28-165 |
| 2I85 | NMR | A=25-166 |
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