Transcription factor SOX-2 (SOX2) is a 317-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P48431.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 59.8 (low 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 | 23% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 24% |
| Below 50 | Very low: often disordered regions | 48% |
What pLDDT means and how to read it
Transcription factor that forms a trimeric complex with OCT4 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206 (By similarity). Binds to the proximal enhancer region of NANOG (By similarity). Critical for early embryogenesis and for embryonic stem cell pluripotency (PubMed:18035408). Downstream SRRT target that mediates the promotion of neural stem cell self-renewal (By similarity). Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation (By similarity). May function as a switch in neuronal development (By similarity)
Interacts with ZSCAN10 (By similarity). Interacts with SOX3 and FGFR1 (By similarity). Interacts with GLIS1 (PubMed:21654807). Interacts with POU5F1; binds synergistically with POU5F1 to DNA (By similarity). Interacts with DDX56 (By similarity). Interacts with L3MBTL3 and DCAF5; the interaction requires methylation at Lys-42 and is necessary to target SOX2 for ubiquitination by the CRL4-DCAF5 E3…
Nucleus speckle, Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6WX8 | X-ray | 2.3 Å | B/D=39-127 |
| 6WX7 | X-ray | 2.7 Å | B=39-127 |
| 6WX9 | X-ray | 2.8 Å | B=39-127 |
| 6T90 | EM | 3.05 Å | L=37-118 |
| 6YOV | EM | 3.42 Å | L=37-118 |
| 9RL4 | EM | 3.5 Å | W=37-118 |
| 9RN2 | EM | 4.1 Å | W=37-118 |
| 9RMC | EM | 4.2 Å | W=37-118 |
| 6T7B | EM | 5.1 Å | K=36-121 |
| 9RN1 | EM | 5.9 Å | W=37-118 |
| 1O4X | NMR | B=39-121 | |
| 2LE4 | NMR | A=39-118 | |
| 9QPF | NMR | A=33-127 |
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