Homework 5

Please find the complex structure of barley lipid transfer protein with
palmitate from PDB.
    1. Find the following data from its header file:
         PDB ID : 1BE2
         Experimental method : NMR, 10 Structures
         Organism (give scientific name) and organ where this protein come
         from : Organism:Hordeum Vulgare,organ:seeds
         Location of its four helixs:
                    HELIX    1 : GLY 4   --> GLY     19
                    HELIX    2 : GLU 26 --> GLN     37
                    HELIX    3 : SER 41 --> ARG     56
                    HELIX    4 : LEU 63 --> CYS     73
         Positions of its four disulfide bonds
                    SSBOND   1: CYS 3   -->   CYS     50
                    SSBOND   2: CYS 13 -->   CYS     27
                    SSBOND   3: CYS 28 --> CYS     73
                    SSBOND   4: CYS 48 --> CYS     87
         Give the chemical formula of the ligand
             C16 H31 O2

2. Show two different views of this protein by Rasmol, one of them
must show its ligand in spacefill display.

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

     4. Measure the bond length of each disulfide bond ( -S-S- ) and calculate the
          average bond length of disulfide bond.
                 cys 3.SG --> cys 50.SG 2.015einstron
                 cys 13.SG --> cys 27.SG 2.015 einstron
                 cys 28.SG --> cys 73.SG 2.016 einstron
                 cys 48.SG --> cys 87.SG 2.015 einstron
                 the average bond length of -S-S- is about 2.015 einstron

5. Show residues in protein that are within 3.0 angstrom of carboxylic
group (COO-) of ligand.

pink--Val17 brown-- Tyr16 yellow--Cys13 green--Leu14
Darkgreen-- Ilu69,Ilu 81