HOMEWORK#3
     Viewing Proteins / PDB
          due on 11/12 

1. Find the structure of prion from PDB. 
	(A) List the following information : 
	(1) ID number:
		1AG2
	(2) Authors:
		M.BILLETER,R.RIEK,G.WIDER,K.WUTHRICH,S.HORNEMANN, R.GLOCKSHUBER
	(3) The number of residues in one monomer:
		Total is 103 residues
		SEQRES   1    103  GLY LEU GLY GLY TYR MET LEU GLY SER ALA MET SER ARG
		SEQRES   2    103  PRO MET ILE HIS PHE GLY ASN ASP TRP GLU ASP ARG TYR
		SEQRES   3    103  TYR ARG GLU ASN MET TYR ARG TYR PRO ASN GLN VAL TYR
		SEQRES   4    103  TYR ARG PRO VAL ASP GLN TYR SER ASN GLN ASN ASN PHE
		SEQRES   5    103  VAL HIS ASP CYS VAL ASN ILE THR ILE LYS GLN HIS THR
		SEQRES   6    103  VAL THR THR THR THR LYS GLY GLU ASN PHE THR GLU THR
		SEQRES   7    103  ASP VAL LYS MET MET GLU ARG VAL VAL GLU GLN MET CYS
		SEQRES   8    103  VAL THR GLN TYR GLN LYS GLU SER GLN ALA TYR TYR

	(4) The number of disulfide bonds:
		SSBOND   1 CYS    179    CYS    214
	(B) Put the structure of prion on your homepages. Show different color for different
	     secondary structure in cartoon form with sidechains on (helix in blue, sheets in red). Show
	     the script that makes the final picture.

	The script is:
	select all
	cartoons
	select helix
	color blue
	select sheet
	color red

Source reference

2. Transcription of the ant gene during lytic growth of bacteriophage P22 is regulated by
     the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Please
     find the co-crystal structure of this Arc tetramer-operator complex from PDB. 

	(a) Make an animation (by Gifbuilder) of whole complex.


	(b) Show the DNA sequences of the Arc operator.
SEQRES   1 E   22    T   A   T   A   G   T   A   G   A   G   T   G   C  1PAR 105
SEQRES   2 E   22    T   T   C   T   A   T   C   A   T                  1PAR 106
SEQRES   1 F   22    A   A   T   G   A   T   A   G   A   A   G   C   A  1PAR 107
SEQRES   2 F   22    C   T   C   T   A   C   T   A   T                  1PAR 108

	(c) The picture below is the hydrogen bonds between beta-sheet side chains and DNA
     bases. Show three side chains (gln9, asn11, arg13) from one monomer and corresponding
     DNA bases of them on your home page. Color three side chain with different color.
     Measure the distance between possible hydrogen bonds.

	After pre-looking for these group,the script is listing:
		Restrict g4f,a5f,t6f,a7f,a8f,a9f,t15e,c16e,t17e,a18e,t19e,c20e,gln9c,gln9d,asn11c,asn11d,arg13c,arg13d
	select gln9
	color green
	select asn11
	color yellow
	select arg13
	color cyan
	show hbond
Source reference