News
Map PDB Structures to Full-length Protein Sequences
12/11
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Protein Feature View from 2vx3's Structure Summary page.
The new Protein Feature View visually summarizes how a full-length protein sequence from UniProtKB corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are also displayed.
For individual entries, the Protein Feature View is available from the Molecular Description Widget on Structure Summary pages. The example shown for PDB ID 2vx3 illustrates how the ranges of a protein that have been observed in an experiment (in blue) correspond to the full length UniProtKB sequence (in grey). The secondary structure information from the PDB entry is also shown (helices in red, beta strands in yellow).
Various features that are known for the UniProtKB sequence are displayed in green as they correlate with regions in the PDB entry. Active sites (from UniProtKB and the PDB entry) are also annotated. Moving the mouse cursor over the "lollipops" displays the residue label. Mousing over the images shown in the "Secstruc" row reveals secondary structure from the PDB entry.
This view can be expanded to map all PDB entries related to a single UniProtKB sequence by selecting the Protein Feature View link shown in this widget. By default, a few representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available. Selecting the plus sign or the "Show All" button will expand the view to show all related PDB chains, which can then be sorted by resolution, length, and release date. These Protein View images can be exported as Scalable Vector Graphics (SVG) files.
The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.
