Tutorials: Working with PKR Data

1. File > Load from PKR

2. The database appears as a table.
   Type in the Organism field: "homo sapiens"

3. All kinases with the organism "homo sapiens" appear as a list.

4. In the Table Menu > Select > Columns

5. Check: "Structure"
   A new column in the table appears that displays whether a structure is available for that Kinase ID.

6. Filtering
   Click "Name."
   This sorts the list of names in alphabetical order.

7. Loading CDK2
   Scroll down to the name cdk2
   Name: cdk2
   Organism: homo sapiens
   PKR ID: 17469
   Notice it has an X-ray structure associated with it. This can be seen in the X-ray column.
   Select the listing.
   Click: "Load"

8. Loading the structure:
   Right click on the "CDK2" name of the sequence.
   Click: "Load Structure"

9. Choose a structure:
   A table showing 53 CDK2 kinases structures is shown.
   Click: "1HCK"
   Click: "OK"

10. In the Sequence Viewer:
    Load from Database
    In the PKR ID field, type "1747"
    Some CDK2 ids will be shown. The numbers 1747 refer to the first four numbers in all CDK2 ids.

11. Load the numbers:
    1747, 17476, 17476
    Hold the shift key and select a few CDK2 sequences.
    Click: Load.

12. The sequences will be automatically aligned due to the Kinase Master Alignment.

13. Color residues by Conservation:
    Click CDK2 in the sequence name field.
    Options > Common Coloring
    Display > Set Residue Color > By Position Conservation
    The sequence and the structure will be colored by Position Conservation.

14. Export:
    File > Export graphics
    Format: ".png"
    Resolution(dpi): "150"
    Choose a file name and location, click: OK

15. Changing the sequence names:
    In the sequence viewer:
    Right Click on "P97377."
    Click: "Rename"
    In the text box type: "CDK2mouse"
    The name of the sequence is changed.

16. Reset sequence color:
    Display > Set residue color > By Default
    The sequence should be black.

17. Conservation Profile:
    Sequence > Conservation Profile
    Sequence Selection Options > Choose all Loaded Sequences
    Position numbering reference > Use Selected Sequence in Loaded Set
    Residue Homology Options > Use Residue Identity
    Click: Execute.

18. A view of the Conservation Profile will be shown.
    Right click in the window.
    Choose "Save image"
    The image should look like the one on the right. Choose a name and a location to save the image.

19. Close the Conservation Profile window.

20. Click on the cdk2 sequence to make it a reference.
    Display > Color by Subdomain
    A rainbow-type structure and sequence is displayed. cdk2 is part of the original structure alignment and the subdomains that were established originally by Hanks and Hunter in 1995 are shown by different colors.
    The structure of cdk2 should also be colored by subdomain since common coloring is still selected.

21. Sequence viewer:
    Display > Set Residue Color > By Default

22. Select the cdk2 sequence.
    Click on residue 13, a Glycine.
    The Glycine should be yellow.
    To select the whole column, click the grey box directly above.
    All glycines in the loaded set of sequences should appear yellow (selected).

23. Show Residue Distribution:
    To show residue distribution within the loaded set:
    Display > Residue Distribution > Within Loaded Set
    Execute.
    To save, right click on the window and save the image in the desired location.
    
    To show residue distribution within the database:
    Display > Residue Distribution > Search Database > Create a New Set
    A Classification Viewer will Open.
    Choose CMGC > CDK.
    Select the box CDK2 and click "Add".
    This adds the all CDK2 ids to a list. To load these ids in the Residue Distribution calculation, click "Load".
    Click "Execute" in the Residue Distribution window.
    The graph to the right should appear as a window.

24. To go onto other tutorials: Tutorial Home.