Bioinformatics HW#5

Please find the complex structure of barley lipid transfer protein with palmitate from PDB.

1. Find the following data from its header file:

(the header of PDB file)

PDB ID

1BE2

Experimental method

NMR

Organism (give scientific name) and organ where this protein come from

The scientific organism name: HORDEUM VULGARE (common name: barley), the organ: SEEDS.

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

(1) Gly4 - Gly19	(2) Glu26 - Gln37	(3) Ser41 - Arg56	(4) Leu63 - Cys73

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

(1) Cys3 - Cys50	(2) Cys13 - Cys27	(3) Cys28 - Cys73	(4) Cys48 - Cys87

Give the chemical formula of the ligand

Palmitic acid: C₁₆H₃₂O₂

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.

The average bond length of 4 disulfide bonds is 2.01 angstroms.

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

Cys13, Leu14, Tyr16, Val17, Ile69, Ile81