Assignment 5 fallback data

 

Please remember: if you use information from this page as a fallback for technical problems with the assignment, you must document this in your submission. State what you tried, what didn't work and only then use the data from here.

   

Target sequence

>MBP1_CHAGL XP_001224558:8..108
AGIYSATYSGIPVYEYQFGPDMKEHVMRRREDNWINATHILKAAGFDKPARTRILERDV
QKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF

CLUSTALW formatted alignment

CLUSTAL alignment

1MB1            NQIYSARYSGVDVYEFIHSTG---SIMKRKKDDWVNATHILKAANFAKAKRTRILEKEV
MBP1_CHAGL      AGIYSATYSGIPVYEYQFGPDMKEHVMRRREDNWINATHILKAAGFDKPARTRILERDV

1MB1            LKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF
MBP1_CHAGL      QKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF

SwissModel response

Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are welcome and help messages. Two other e-mail messages conatin the program output and the model.

• SwissModel Program Output
• SwissModel attached Model Coordinates

LGA superposition

The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.

1. LGA created several END records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains in MODEL and ENDMDEL, which prevents bonds between being drawn.

• LGA superposition report
• 1DUX_1MB1 Coordinates

Protein-DNA complex model

The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.

• Model/DNA complex Coordinates