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![[Figure 2]](nz5018fig2mag.jpg)
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Figure 2
Barbed wire residues in AlphaFold2 predictions. (a) Nearly all-barbed wire prediction of fragment 6 of UniProt ID Q86YZ3 (very long sequences are predicted as multiple overlapping fragments). Wide, looping or tangled coils are typical of the barbed-wire prediction mode. (b) Real barbed wire, whose spikes and coils give the prediction mode its name. (Image credit: Smithers7 by way of Wikimedia Commons, Creative Commons Attribution 3.0 Unported). (c) Zoomed-in view of the Q86YZ3 fragment 6 prediction, residues 962–1005, with MolProbity validation markup, showing an extremely high density of validation outliers. Markup is green for Ramachandran outliers, red and blue for covalent geometry outliers, magenta for CaBLAM, lime green and yellow for cis and twisted peptide bonds. CA geometry outliers from CaBLAM are omitted for clarity but are pervasive. Carbonyl oxygen bonds are frequently pointed in the same direction, rather than alternating as in β-strands. (d) Ramachandran distribution for general-case residues in the Q86YZ3 fragment 6 prediction. Outliers are marked in purple. The distribution is highly unusual and clustered in the upper right of the plot, corresponding to an extended but unprotein-like conformation. |
![[Figure 2]](nz5018fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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