Homeobox protein Nkx-2.5 (NKX2-5) is a 324-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P52952.
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The mean pLDDT of this model is 62.6 (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 | 17% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 34% |
| Below 50 | Very low: often disordered regions | 38% |
What pLDDT means and how to read it
Transcription factor required for the development of the heart and the spleen (PubMed:22560297). During heart development, acts as a transcriptional activator of NPPA/ANF in cooperation with GATA4 (By similarity). May cooperate with TBX2 to negatively modulate expression of NPPA/ANF in the atrioventricular canal (By similarity). Binds to the core DNA motif of NPPA promoter (PubMed:22849347, PubMed:26926761). Together with PBX1, required for spleen development through a mechanism that involves CDKN2B repression (PubMed:22560297). Positively regulates transcription of genes such as COL3A1 and MMP2, resulting in increased pulmonary endothelial fibrosis in response to hypoxia (PubMed:29899023)
Homodimer (via the homeobox); binds DNA as homodimer (PubMed:22849347). Interacts (via the homeobox) with TBX5 (via the T-box); this complex binds DNA (PubMed:26926761). Interacts with HIPK1 and HIPK2, but not HIPK3. Interacts with the C-terminal zinc finger of GATA4 through its homeobox domain. Also interacts with JARID2 which represses its ability to activate transcription of ANF. Interacts…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3RKQ | X-ray | 1.7 Å | A/B=138-194 |
| 6WC2 | X-ray | 2.1 Å | M/N/O=137-197 |
| 4S0H | X-ray | 2.82 Å | B/F=142-194 |
| 6WC5 | X-ray | 2.9 Å | I/N=140-196 |
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