Slide 1Powerpoint Assignment for Micbio 565

• Eric Martz• Yeast Gal4 transcriptional

regulator, 1d66.• X-ray crystallography,

resolution 2.7 Angstroms.• 2 protein chains + 2 DNA

chains (total 4)

Slide 2: PQS• The published PDB file has 4 chains.• PQS says “dimeric complex”, meaning a protein dimer complexed to DNA (still 4 chains).

Published PQS

Slide 3: Ligands

Abbreviation Full Name

CD Cadmium ion

Slide 4: Hydrophobic/Polar• This protein has a mostly polar surface, consistent with it

being water soluble. There are no large hydrophobic patches on its surface.

Slide 5: Charge• The DNA-binding notch in the protein has only positive

charge, consistent with the need to bind the negatively-charged phosphate backbone of the DNA.

Slide 6: Conservation (ConSurf)

The amino acids that contact the major groove of the DNA are highly conserved. This is where Lysine 18 (highlighted) recognizes the specific DNA sequence CGG.

Slide 7: Animation from Polyview-3D

Lysine 18 in Gal4 sits in the major groove of DNA, recognizing the DNA sequence CGG.

This animation was kept small to minimize the load on the Polyview-3D server. It rocks through 90 degrees in 2 degree steps, with a 5/100 second delay.

Optional Slide 8:Noncovalent Bonds

• 6 cysteine sulfurs form a cage around the two cadmium metal ions.