 | Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
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![[Figure 3]](yg5009fig3mag.jpg)
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Figure 3
Structural comparison of the AlphaFold model and crystal structure of PgDUF2436. (a) The predicted aligned error (PAE) plots are shown as a heatmap image with color-coded high confidence (blue) to low confidence (red), where the x and y axes correspond to residues. (b) The top-ranked AlphaFold model rank_1 is shown as a cartoon, colored by the predicted local distance difference test (plDDT) score, ranging from blue (over 90) to red (less than 50). The dashed yellow and cyan lines indicate the subdomain boundaries in the AlphaFold model. The yellow dotted box highlights the region from Asn384 to Glu525, while the cyan-colored dotted box indicates the region from Tyr535 to Cys579. (c) The plDDT score is plotted per residue for the top five ranked AlphaFold models. (d) Superposition of the experimentally determined PgDUF2436 domain structure (green, secondary-structure labeling in white text with a green border) with the AlphaFold prediction model (gray). (e) Secondary-structure alignment of PgDUF2436 and rank_1. The largest difference in the comparison between the crystal structure and the AlphaFold model (rank_1) of PgDUF2436 is the determination of domain boundaries. The rank_1 structure predicted that the PgDUF2436 domain consists of β0–β11 (residues Glu385–Asp526), but the actual crystal structure shows that the PgDUF2436 domain is composed of β1–β10 (residues Asp369–Arg513). The region corresponding to residues Met516–Cys579 (β11–β15) was absent from the actual PgDUF2436 crystal structure because of very weak electron density. |
![[Figure 3]](yg5009fig3.jpg)
| STRUCTURAL BIOLOGY COMMUNICATIONS |
ISSN: 2053-230X
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