452 Homework 1: Protein scavenger hunt from the PDB!(16)Name:                      .
Find the information requested below for your personal protein, PDB#=        1dfn                                        .

You can print out the information instead of rewriting it, but be sure to indicate where it is in the space below. Everything you need can be found through the PDB site: http://www.rcsb.org/pdb/
 
 

a. identify the basic 3-D "anatomy" type of the protein (class, fold, etc. e.g. all alpha, cytochrome c fold) found through SCOP ( http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.1.html )or CATH (see "Structural Neighbors" at PDB site).
 
 
 
 

b. print out and attach the secondary structure display structure of your protein using "FirstGlance" (through "View Structure").
 
 
 
 

c. find the amino acid sequence
 
 

d. who are the authors on this study (who determined the structure?
 
 
 
 

e. is the protein found as a monomer or in some other association?
 
 
 
 

f. predict secondary structure from the sequence with a program designed to predict secondary structure from only amino acid sequence. Find it at the address below (SSCP Web site) and paste in your sequence (from "Sequence Details" at the PDB; copy in FASTA format). Attach the report to this paper.

http://www.bork.embl-heidelberg.de/SSCP/sscp_seq.html
 
 

g. Compare the theoretical results with the known secondary structure (you can get this from "Sequence Details" at the PDB). How well did this prediction work?
 
 
 
 
 
 

h. tell me one more cool bit of information and/or graphical representation that you can get through this site and attach the printout to show me.