General control transcription factor GCN4 (GCN4) is a 281-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P03069.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 66.7 (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 | 19% |
| 70 to 90 | Confident: backbone generally right | 22% |
| 50 to 70 | Low: treat with caution | 38% |
| Below 50 | Very low: often disordered regions | 21% |
What pLDDT means and how to read it
Master transcriptional regulator that mediates the response to amino acid starvation (PubMed:11390663, PubMed:29628310). Binds variations of the DNA sequence 5'-ATGA[CG]TCAT-3' in canonical nucleosome-depleted 5'-positioned promoters, and also within coding sequences and 3' non-coding regions (PubMed:11390663, PubMed:1473154, PubMed:1939099, PubMed:2204805, PubMed:2277632, PubMed:29628310, PubMed:3530496, PubMed:3532321, PubMed:3678204, PubMed:7664107). During nutrient starvation (low or poor amino acid, carbon or purine sources), it activates genes required for amino acid biosynthesis and transport, autophagy, cofactor biosynthesis and transport, mitochondrial transport, and additional…
Homodimer (PubMed:1473154, PubMed:3678204). Each subunit binds overlapping and non-identical half-sites that flank the central CG base-pair in the pseudo-palindromic motif 5'-ATGA[CG]TCAT-3' (PubMed:1473154, PubMed:2204805, PubMed:3678204, PubMed:7664107). Interacts with the mediator tail; the interaction with GAL11/MED15 is direct (PubMed:10549298, PubMed:19940160, PubMed:9488488). Interacts…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3AZD | X-ray | 0.98 Å | A/B=250-281 |
| 2WQ1 | X-ray | 1.08 Å | A=249-281 |
| 2WQ0 | X-ray | 1.12 Å | A=249-281 |
| 4OWI | X-ray | 1.2 Å | A/B=248-278 |
| 2WQ3 | X-ray | 1.22 Å | A=249-281 |
| 2HY6 | X-ray | 1.25 Å | A/B/C/D/E/F/G=251-281 |
| 2WPZ | X-ray | 1.25 Å | A/B/C=249-281 |
| 6PSA | X-ray | 1.3 Å | A=249-277 |
| 2IPZ | X-ray | 1.35 Å | A/B/C/D=251-281 |
| 2YNY | X-ray | 1.35 Å | A/B/C=250-278 |
| 5APU | X-ray | 1.35 Å | A/B/C=250-281 |
| 2WQ2 | X-ray | 1.36 Å | A=249-281 |
| 5APS | X-ray | 1.37 Å | A=250-281 |
| 2NRN | X-ray | 1.4 Å | A/B/C/D=248-281 |
| 2YNZ | X-ray | 1.4 Å | A/B/C=250-278 |
| 7OAA | X-ray | 1.4 Å | A=248-277, A=250-278 |
| 3M48 | X-ray | 1.45 Å | A=249-281 |
| 7OAF | X-ray | 1.45 Å | A/B/C=248-277, A/B/C=250-278 |
| 1LLM | X-ray | 1.5 Å | C/D=250-281 |
| 2B1F | X-ray | 1.5 Å | A/B/C/D=251-281 |
Showing 20 of 168 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.