homework1

Homework 2

Kevin Lee, a graduate student in the department of life sciences, has purified a protein from rice. Here is the sequence of this protein -

ITCGQVNSAVGPCLTYARGGAGPSAACCSGVRSLKAAASTTADRRTACN

CLKNAARGIKGLNAGNAASIPSKCGVSVPYTISASIDCSRVS

1. Please help him to identify this protein in PDB.

Answer: RICE NONSPECIFIC LIPID TRANSFER PROTEIN

2. Find the following data from its header file:

Answer:

PDB ID
1ZRL
Experimental method
X-RAY DIFFRACTION
Location of its four helixs
Cys3 -- Ala17, Ala25 -- Ala37, Thr41 -- Arg56, Ala63 -- Cys73
Positions of its four disulfide bonds
Cys3 -- Cys50, Cys13 -- Cys27, Cys28 -- Cys73, Cys48 -- Cys87
Name of the hetero atoms
SO4, HOH, CXS

3. Show two diferent views of this protein by Rasmol.

4. Show protein in cartoon with its four disulfide bonds in yellow color.

5. Measure the bond length of each disulfide bond ( -S-S- ) and calculate the average bond length of disulfide bond.

Answer: (2.02 A + 2.02 A + 2.01 A + 2.00 A)/4 = 2.0125 A