HOMEWORK5

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_scientific	Hordeum Vulgare
Organism_common	Barley
Organ	Seeds

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

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 ( i.e. Cys3 - Cys24)

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

CH₃(CH₂)₁₄COOH 

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.

1-2：16.480

1-3：20.944

1-4：10.292

2-3：9.667

2-4：17.472

3-4：17.949

average bond length：13.856

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