Mediator of DNA damage checkpoint protein 1 (MDC1) is a 2089-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q14676.
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The mean pLDDT of this model is 40.3 (very 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 | 13% |
| 70 to 90 | Confident: backbone generally right | 1% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 85% |
What pLDDT means and how to read it
Histone reader protein required for checkpoint-mediated cell cycle arrest in response to DNA damage within both the S phase and G2/M phases of the cell cycle (PubMed:12475977, PubMed:12499369, PubMed:12551934, PubMed:12607003, PubMed:12607004, PubMed:12607005, PubMed:12611903, PubMed:14695167, PubMed:15201865, PubMed:15377652, PubMed:16049003, PubMed:16377563, PubMed:30898438). Specifically recognizes and binds histone H2AX phosphorylated at 'Ser-139', a marker of DNA damage, serving as a scaffold for the recruitment of DNA repair and signal transduction proteins to discrete foci of DNA damage sites (PubMed:12607005, PubMed:15201865, PubMed:16049003, PubMed:16377563, PubMed:30898438). Also…
Homodimer (PubMed:22234877). Interacts with H2AX, which requires phosphorylation of H2AX on 'Ser-139' (PubMed:15201865, PubMed:16049003, PubMed:16377563, PubMed:20159462). Interacts with the MRN complex, composed of MRE11, RAD50, and NBN (PubMed:12607003, PubMed:12607005). Interacts with CHEK2, which requires ATM-mediated phosphorylation of 'Thr-68' within the FHA domain of CHEK2…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2ETX | X-ray | 1.33 Å | A/B=1884-2089 |
| 3K05 | X-ray | 1.33 Å | A/B=1891-2089 |
| 2ADO | X-ray | 1.45 Å | A/B=1891-2086 |
| 3UMZ | X-ray | 1.65 Å | A/B=27-138 |
| 3UNN | X-ray | 1.7 Å | A=27-138, B=1-8 |
| 3UNM | X-ray | 1.8 Å | A/B=27-138 |
| 3UOT | X-ray | 1.8 Å | A/B=19-138, D/E=1-10 |
| 3UN0 | X-ray | 2.3 Å | A/B=26-138 |
| 9QJZ | X-ray | 2.31 Å | C/D=943-958 |
| 2AZM | X-ray | 2.41 Å | A/B=1883-2089 |
| 9IF9 | X-ray | 2.55 Å | C/D=761-769 |
| 3UEO | X-ray | 2.6 Å | E/F=325-336 |
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