![pymol tutorial reaction pymol tutorial reaction](https://secureservercdn.net/160.153.137.210/8b7.f6c.myftpupload.com/wp-content/uploads/2017/01/cropped-image8-3.png)
It shows among other things the experimentally determined positions (atomic coordinates) of all the atoms in the model (including many water molecules). Take a look at the pdb-file, for example in WordPad. Save it, for example on the Desktop, as 1ebm.pdb.
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Click on Download Files (up at the right hand side) and download the PDB textįile. Possibly they were not able to crystallize the full-length protein. One likely reason why the researchers behind this study removed these two segments is that they are structurally disordered. Residues 1 to 11 and 326 to 345 have been removed. It is a K249Q mutant which means Lys249 has been mutated to Gln.
![pymol tutorial reaction pymol tutorial reaction](https://mmbios.pitt.edu/images/highlights/QMMM2.jpg)
There are 3 chains, A (OGG1 protein), C and D (two strands of DNA). We usually consider a DNA duplex to be one macromolecule even if the two strands are not covalently connected, thus 2 macromolecules in total. Is it a full-length protein? What is missing? Do you have any suggestions for why it is not full-length? (Hint: Structural disordered regions are hard to crystallize)ġEBM contains a DNA duplex and a protein, OGG1.
![pymol tutorial reaction pymol tutorial reaction](https://www.cipsm.de/site/assets/files/6046/habazettl_et_al_w_supporting_500.jpg)
Which macromolecules does this structure contain? How many chains are there? What is chain A? Is it mutated? Do you have any suggestions for why the researchers behind this study have mutated a single residue? If not, you will have the chance to guess later in this Exercise. Only one hit, so you are sent directly to the Structure Summary for this structure. Type in 1EBM in the search field and press enter to search for this structure. There are various ways to search the database, the most common being by protein name, acronym, organism, protein class or author name.Ĥ. Here you can search for protein structures determined by either X-ray crystallography or NMR. Open a browser window and go to the PDB at. There is lots of more useful information and links in the PDBsum database that you might investigate when you have time.ģ. Asp174 is certainly in a loop since it is not in the alpha-helical or beta-sheet regions. There is an unfavorable conformation for the protein backbone here. It is a region of the Ramachandran plot that is not preferred for a non-Gly residue. 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?Ģ7 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.
![pymol tutorial reaction pymol tutorial reaction](https://sites.google.com/site/gtkdynamo/_/rsrc/1472848600890/tutorials/6---enzyme-reaction/QCAtoms.001.jpg)
In this Exercise we will use the visualization program PyMOL and also have a look at some online resources for structural data.