Serine/threonine-protein kinase VRK1 (VRK1) is a 396-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q99986.
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The mean pLDDT of this model is 85.0 (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 | 74% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 17% |
What pLDDT means and how to read it
Serine/threonine kinase involved in the regulation of key cellular processes including the cell cycle, nuclear condensation, transcription regulation, and DNA damage response (PubMed:14645249, PubMed:18617507, PubMed:19103756, PubMed:33076429). Controls chromatin organization and remodeling by mediating phosphorylation of histone H3 on 'Thr-4' and histone H2AX (H2aXT4ph) (PubMed:31527692, PubMed:37179361). It also phosphorylates KAT5 in response to DNA damage, promoting KAT5 association with chromatin and histone acetyltransferase activity (PubMed:33076429). Is involved in the regulation of cell cycle progression of neural progenitors, and is required for proper cortical neuronal migration…
Interacts with HDAC1, KAT2B, SETDB1, KDM3A and KDM4A (PubMed:37179361). Associates with the nucleosome through interactions with nucleosome DNA, histone H2A and histone H2B; the interaction with H2A and H2B is mediated by the nucleosome acidic patch, a cluster of negatively charged residues of H2A and H2B forming a cleft within the nucleosome core (PubMed:35390161)
Nucleus, Cytoplasm, Nucleus, Cajal body
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7M10 | X-ray | 1.15 Å | B=2-13 |
| 6BRU | X-ray | 1.8 Å | A/B/C/D=3-364 |
| 6BU6 | X-ray | 1.8 Å | A/B/C/D=3-364 |
| 6BP0 | X-ray | 1.9 Å | A/B/C/D=3-364 |
| 6BTW | X-ray | 1.9 Å | A/B/C/D=3-364 |
| 5UVF | X-ray | 2.0 Å | A/B/C/D=3-364 |
| 6CNX | X-ray | 2.0 Å | A/B/C/D=3-364 |
| 6VXU | X-ray | 2.0 Å | A/B/C/D=3-364 |
| 9ZKG | X-ray | 2.06 Å | A/B/C/D=3-364 |
| 6AC9 | X-ray | 2.07 Å | A/B/C/D=1-364 |
| 6CMM | X-ray | 2.1 Å | A/B/C/D=3-364 |
| 6DD4 | X-ray | 2.1 Å | A/B/C/D=3-364 |
| 6CQH | X-ray | 2.15 Å | A/B/C/D=3-364 |
| 6NPN | X-ray | 2.2 Å | A/B/C/D=3-364 |
| 6CSW | X-ray | 2.25 Å | A/B/C/D=3-364 |
| 8V42 | X-ray | 2.3 Å | A/B/C/D=3-364 |
| 3OP5 | X-ray | 2.4 Å | A/B/C/D=3-364 |
| 5UKF | X-ray | 2.4 Å | A/B/C/D=3-364 |
| 6CFM | X-ray | 2.45 Å | A/B/C/D=3-364 |
| 6VZH | X-ray | 2.55 Å | A/B/C/D=3-364 |
Showing 20 of 26 experimental structures (best resolution first).
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