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![[Figure 5]](nz5018fig5mag.jpg)
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Figure 5
Examples of low-pLDDT pseudostructure predictions from UniProt ID O15353, human forkhead box protein N1. (a) Overall prediction colored by pLDDT from the Mol* viewer at the AlphaFold Database. A well packed and well predicted core is surrounded by barbed wire and pseudostructure. Several pseudostructure elements are sufficiently similar to secondary structure to be depicted as ribbons by Mol*. (b) A pseudostructure helix, residues 544–554. Hydrogen bonding (light green dots arranged in pillow shapes) is inconsistent or weak, and the helix is not well formed. A γ-turn-like segment, a rare pseudostructure feature, is visible before/below the helix. (c) A pseudostructure β-strand, residues 161–169. This strand is unpaired, so has no hydrogen bonding. Barbed wire regions before and after the strand show the sharp difference in validation outlier density, even though all of this strand is predicted at very low confidence (mostly pLDDT < 40). (d) A polyproline II region, residues 464–470. This conformation is correctly associated with regions of high proline content in AlphaFold predictions, but often occurs with low pLDDT. |
![[Figure 5]](nz5018fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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