Type 1 encapsulin shell protein EncA (encA) is a 287-residue protein from Myxococcus xanthus (strain DK1622). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q1D6H4.
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The mean pLDDT of this model is 82.0 (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 | 22% |
| 70 to 90 | Confident: backbone generally right | 64% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
Shell component of a type 1, iron-storage encapsulin nanocompartment. Encapsulin nanocompartments are 32 nm in diameter with an iron- and phosphorus-rich core (4Fe:1P) about 24 nm in diameter. Upon expression in E.coli most particles are 32 nm, 20% are 18 nm. The core is filled with an average of 14 dense granules, 5-6 nm in diameter that are not evenly distributed. Each nanocompartment is estimated to hold 30,000-35,000 Fe atoms (PubMed:25024436, PubMed:31194509). The minor proteins EncB, EncC and EncD probably lie against the interior face of the nanocompartment (Probable)
The 32 nm encapsulin nanocompartment is formed by 180 subunits; monomers form pentamers which assemble to form shells. There are 36 pores where the pentamers meet as well as 3-fold axis channels and dimer channels. The N-terminus of the protein is inside the shell
Encapsulin nanocompartment
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8VJO | EM | 2.4 Å | A/B/C=1-287 |
| 8V4N | EM | 2.43 Å | A=1-287 |
| 8TK7 | EM | 2.53 Å | A/B/C=1-287 |
| 8V4Q | EM | 2.71 Å | A/B/C=1-287 |
| 9B9I | EM | 2.86 Å | A=1-287 |
| 7S4Q | EM | 3.12 Å | A/B/C=1-287 |
| 9B9Q | EM | 3.14 Å | A/B/C=1-287 |
| 7S20 | EM | 3.4 Å | A/B/C=1-287 |
| 7S21 | EM | 3.4 Å | A=1-287 |
| 7S2T | EM | 3.45 Å | A/B/C=1-287 |
| 9BC8 | EM | 3.46 Å | A/B/C/D=1-287 |
| 4PT2 | EM | 4.6 Å | A/B/P=1-287 |
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