Please answer the following questions about this protein: Urokinase -(type plasm
ID: 834969 • Letter: P
Question
Please answer the following questions about this protein:
Urokinase -(type plasminogen activator (OmpX))
Please answer in DETAIL without using pictures.
1. Describe the overall structure of the protein.
2. Describe the distribution of polar and nonpolar residues around the helix. Make a table make is
polar or nonpolar below or above the H part.
3. Describe the location of the helix and relate its location to the distribution of residue types as
shown in number 2. Talks about secondary structure.
4. Describe the distribution of polar and nonpolar residues on opposite sides of the sheet. Talks
about betapleated sheet
5. Describe the location of the sheet and relate its location to the distribution of residue types as
shown in number 4.
6. Make a table of hydrogen bonds that hold the hetero group, i.e. ligand, to the protein. For each
bond, list the donor and acceptor atoms (for example NH of Gly32 or OD2 of Asp54) and the
distance (I have ADDED this measurement to the table, not listed on the webpage). Also, what
is the role of the ligand for your particular protein? The easiest place to find out is the reference
given in the original pdb file.
7. Label all the residues that make non-polar contacts. List these residues in a table.
8. Prepare as described. Then, as suggested, render the molecule as a solid, including the ribbons.
Explanation / Answer
1.)
Protein structure is the biomolecular structure of a protein molecule. Proteins are polymers