Protein code: 2W17
– which is (CKD2),
Describe the therapeutic relevance of your protein. Eg. Any disorders associated with the protein, drugs/inhibitors & how they work at the molecular level.
All student must include self-prepared images using one of the online molecular viewing software applications outlined in the Supplementary information (not cut & pasted from other sources) showing something specific & relevant to each student’s presentation.
– prepared images showing relevant details for your particular focus.
Software
There are numerous freeware programs for visualising & displaying various features of molecules. Some examples are PyMOL, UCSF Chimera, JMOL or web-based such as EzMol.
Visualising Molecules and Preparing images:
The PDB website itself can produce some relevant images. Either of the entire protein or a close up of key interactions with the ligand.
EzMOL (http://www.sbg.bio.ic.ac.uk/~ezmol/)
Enter your 4 digit code.
Play around with the protein once it’s loaded: rotate it with the mouse to see aspects of the backbone ribbon, general 3D shape and position of any ligands.
There are 8 Steps in which you can display certain features of the molecule differently, create surfaces, highlight important residues of interest, etc. Spend time going through them.
For example, click on Step 2 and click on the various ways the protein can be displayed. Including stick showing amino acid residues and surface showing the contours of the surface. Certain characteristics of the surface (lipophilicity/electrostatics etc) can further enhance this type of display. Note the position of the ligand in the binding site.
When you’ve completed a display and want to save/capture it, click on Step 8 for a larger size image. Then you can save the image, save your work log.