On the NCBI home page, click TaxBrowser on the black bar at the top.
In the left blue side bar, click Taxonomy browser.
Type "horseshoe crab" in the box and set the menu to "token set".
Click Go.
Find structure records for a single species
In the results list, click on the common name "Atlantic horseshoe crab".
In the table, click on the number of structure records.
Refine the set of structure records
Add the following to the current query in the search box: AND 1.0:1.5[resolution] and click Go.
Find the record in the list labeled as a transition state and click on the accession number to open the structure summary page.
Find ligands linked to the structure record
Scroll down to the bottom of the page and make a note of the heterogens present.
Locate relevant literature about a structure
Click on the "All References" link at the top of the page, and then open the 1998 abstract by Zhou et al.
Make a note of the comments about the positioning of the bound ligands.
Locate and identify heterogens in a structure
Return to the structure summary page by going back twice in your browser, and click the structure image.
Choose Style / Coloring Shortcuts / Molecule
Locate the three heterogens next to the magnesium (Mg) ion. They will each be colored differently. Note their
relative locations.
Locate a bound co-factor
Zoom in and locate the nitrate ion bound to the Mg ion. (Nitrate has four atoms, and is directly bound to Mg).
Double click on the nitrate ion (it should turn yellow).
Locate binding site residues
Choose Show/Hide / Select by Distance / Residues Only and set the distance to 4.5 Angstroms.
Find the five arginines among the highlighted residues. Holding down the Control key, click on the highlighted
residues that are NOT arginine to deselect them.
Create a custom annotation
Choose Style / Annotate, click "New", and give the annotation the name "Arg".
Click Edit Style, check the protein side chain box, and render them as "Tubes" with a color of your choice.
Label residues in the annotation
Click the Labels tab and set the protein backbone spacing to 1 and the type to One Letter.
Click Done, OK, and then Done. Now deselect the residues to see the annotated color.
Add a second annotation
The catalytic residue is thought to be either E225 or E314. Using Style / Annotate, create a new annotation where the sidechains of these residues are rendered as ball-and-stick models colored by charge. Label these with one letter labels as before.
Save your work
Experiment with turning the annotations on and off in the Annotation panel. You can now save the annotated file for future use.
