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

SOURCE   2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE SOURCE   3 ORGANISM_COMMON: BARLEY;
SOURCE   4 ORGAN: SEEDS
• Location of its four helixs (i.e. Ala12 - Gly20)

HELIX    1   1 GLY      4  GLY     19
HELIX    2   2 GLU     26  GLN     37
HELIX    3   3 SER     41  ARG     56
HELIX    4   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
C16 H32 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.

Cys13(CA)--Cys27(CA):6.323
Cys3(CA)---Cys50(CA):5.673
Cys87(CA)--Cys48(CA):5.623
Cys73(CA)--Cys28(CA):4.394
Average=5.503

 

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

　
 
 

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