Visualization of a 3D structure using RasTop

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Visualization of a 3D structure using RasTop
Download the program here http//www.geneinfinity
.org/rastop/download
Open the PDB file 2J5F
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RasTop
Default visualization color by secondary
structures, show all hetero atoms
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RasTop Ribbons menu
Try different presentations Choose Display Only
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RasTop Atom Selection
Click here to open the selection window
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RasTop Display buttons
Click here to display the ligand in different
presentations
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RasTop Color
Color the atoms of the ligand by their type
(CPK) Try also to select the protein and change
its color
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Rastop Select Within
Select the atoms around the ligand (radius of 4
angstroms1000 R.U.)
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Rastop Display options
Color the selection in red and display as spheres
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RasTop Restrict
Click Restrict to show only the selected atoms
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Rastop Selections
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Rastop Distance monitor
http//www.expasy.org/uniprot/P00533
1. What is the ATP binding residue? Look in
expasy- under the features section.
2. Restrict the ligand and the ATP binding
residue, display as balls sticks, color by CPK
and zoom.
3. Click the monitor tool and select two atoms to
measure the distance between them.