The Gly residues (blue triangles) are distributed more widely in the plot. The 19 non-Gly residues (blue squares) are mainly localized in the alpha-helical and beta-sheet regions, in the red and brown regions (the most preferred regions) of the Ramachandran plot. OGG1 contains more -helices than -sheets. There are many more points (blue dots) in the alpha-helical region than in the beta-sheet region. Does this protein mainly contain -helices, -sheets, or loops/coils? Do the Gly residues (shown as blue triangles) have a different distribution from all other residues (shown as blue squares)? One single residue is shown in red. Click on the picture under Procheck to get a look at the Ramachandran plot for 1EBM. Right!), an alternative structure database to the PDB.

For the structure 1EBM, follow the link to the PDBsum database (the column at the With a resolution ~1.6 or worse one cannot reliably predict the positions of the H atoms from the electron density. The only full-length structures are 1KO9 and 2XHI. How many structures are listed for OGG1? What is the PDB identifier for the structure with the best resolution? Are any of the structures for the full-length protein? Are there any hydrogen atoms in any of the structures? Why not?Дў7 structures for human OGG1. Quite far down on the page you will find links to 3D structure databases. In the isoform -OGG1 (Isoform 1A) there are 345 residues.

You can find information on the protein 8-oxoguanine DNA glycosylase, human OGG1. If you also have used PyMOL before or even done this exercise (very thoroughly) previously, you can jump directly to for example item 32. If you have a lot of experience using UniProt, PDBSum, and the PDB you may browse quickly through the first items below or skip directly to item 7. In this Exercise we will use the visualization program PyMOL and also have a look at some online resources for structural data.

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