Methyl-CpG-binding domain protein 2 (MBD2) is a 411-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9UBB5.
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The mean pLDDT of this model is 67.0 (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 | 31% |
| 50 to 70 | Low: treat with caution | 18% |
| Below 50 | Very low: often disordered regions | 35% |
What pLDDT means and how to read it
Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides (PubMed:9774669). Binds hemimethylated DNA as well (PubMed:10947852, PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases to chromatin (PubMed:10471499, PubMed:10947852). Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin (PubMed:16428440, PubMed:28977666). Acts as a transcriptional repressor and plays a role in gene silencing (PubMed:10471499, PubMed:10947852, PubMed:16415179). Functions as a scaffold protein, targeting GATAD2A and GATAD2B to chromatin to promote repression (PubMed:16415179). May…
Heterodimer with MBD3 (via N-terminus) (PubMed:10947852, PubMed:15701600). Component of the MeCP1 complex that contains HDAC1 and HDAC2 (PubMed:10471499, PubMed:11102443). Component of the nucleosome remodeling and deacetylase (NuRD) repressor complex, composed of core proteins MTA1, MTA2, MTA3, RBBP4, RBBP7, HDAC1, HDAC2, MBD2, MBD3, and peripherally associated proteins CDK2AP1, CDK2AP2,…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7MWM | X-ray | 1.6 Å | A/B=143-220 |
| 7RAY | X-ray | 1.78 Å | A=143-220 |
| 6C1T | X-ray | 1.84 Å | A/D=143-220 |
| 6C1A | X-ray | 2.05 Å | A/B/E/F=143-220 |
| 6CNP | X-ray | 2.1 Å | A/B=143-220 |
| 6CNQ | X-ray | 2.15 Å | A/B=143-220 |
| 6C1U | X-ray | 2.3 Å | A/B/E/F=143-220 |
| 6C1V | X-ray | 2.3 Å | A/B/E/F=143-220 |
| 7MWK | X-ray | 2.45 Å | A/B=143-220 |
| 6C2F | X-ray | 2.65 Å | A/D/G/J/M/P=143-220 |
| 7AO8 | EM | 4.5 Å | C=1-411 |
| 7AO9 | EM | 6.1 Å | C=1-411 |
| 7AOA | EM | 19.4 Å | C=1-411 |
| 2L2L | NMR | B=360-393 |
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