O-GlcNAcase NagJ (nagJ) is a 1001-residue protein from Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q0TR53.
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The mean pLDDT of this model is 93.1 (very high 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 | 89% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
Binds carbohydrates (PubMed:16990278). Capable of hydrolyzing the glycosidic link of O-GlcNAcylated proteins. Can bind and deglycosylate O-glycosylated peptides from mammals
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2J1A | X-ray | 1.49 Å | A=623-767 |
| 2OZN | X-ray | 1.6 Å | A=768-909 |
| 2W1N | X-ray | 1.8 Å | A=765-1001 |
| 2V5C | X-ray | 2.1 Å | A/B=31-624 |
| 2VUR | X-ray | 2.2 Å | A/B=31-624 |
| 2CBI | X-ray | 2.25 Å | A/B=31-624 |
| 2X0Y | X-ray | 2.25 Å | A/B=31-624 |
| 2J62 | X-ray | 2.26 Å | A/B=31-624 |
| 2J7M | X-ray | 2.3 Å | A=623-767 |
| 7KHV | X-ray | 2.3 Å | A/B/C/D/E/F=31-624 |
| 2WB5 | X-ray | 2.31 Å | A/B=31-624 |
| 2CBJ | X-ray | 2.35 Å | A/B=31-624 |
| 2J1E | X-ray | 2.4 Å | A=623-767 |
| 2XPK | X-ray | 2.4 Å | A/B=31-624 |
| 2JH2 | X-ray | 2.5 Å | A/B/C=764-909 |
| 2YDS | X-ray | 2.55 Å | A=31-618 |
| 2YDQ | X-ray | 2.6 Å | A=31-618 |
| 4ZXL | X-ray | 2.6 Å | A=39-617 |
| 5OXD | X-ray | 2.6 Å | A=31-618 |
| 2YDR | X-ray | 2.75 Å | A=31-618 |
Showing 20 of 23 experimental structures (best resolution first).
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