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.

Rice nonspecific lipid transfer protein

2. Find the following data from its header file:

• PDB ID

1RZL

• Experimental method

X-ray diffraction. Temp. 290 K. pH-7.8

• Location of its four helixs (i.e. Ala12 - Gly20)

Cys 3-Ala 17

Ala 25-Ala 37

Thr 41-Arg 56

Ala 63-Cys 73

• Positions of its four disulfide bonds ( i.e. Cys3 - Cys24)

Cys 3-Cys 50

Cys 13-Cys27

Cys 28-Cys 73

Cys 48-Cys 87

• Name of the hetero atoms

CXS   :  3-cyclohexyl-1-propylsulfonic acid

SO^4- :  sulfate ion

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.

Cys 3-Cys 50 ---2.022 A

Cys 13-Cys27 ---2.010 A

Cys 28-Cys 73 ---2.021 A

Cys 48-Cys 87 ---2.014 A

Average bond length ---2.01675 A