HOMEWORK 3

Viewing Proteins / PDB

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1. Find the structure of trp repressor complexed with its operator from PDB

(1) ID number:1TRO

(2) Authors:Z.Otwinowski, R.G. Zhang, P.V.Sigler

(3) Resolutions:1.9A

(4) How many residues in one monomer:108

(5) How many cofactors in whole complex: 4

Show the complex molecule on your homepages. Show different color for different chain in cartoon form. Indicate all the cofactors in spacefill form and blue color. Show the script that makes the final picture.

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.

1E:TATAGTAGAGTGC

2E:TTCTATCAT

1F:AATGATAGAAGCA

2F:CTCTACTAT

(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.

The total region:

The H-bonds of the C subunit part of the region:

The H-bonds of the D subunit part of the region: