CS 640
Assignment #1 Example of Images
Using Pymol for Visualization of Biological Macromolecules
Do NOT report on this protein. This is merely an example of what I am looking for in the
two images you create for your report. Your report will contain more text (1 page) than
this example.
The protein below is involved in apoptosis; it is the apoptotic protease activating factor, or Afap1,
whose structure was solved by X-ray crystallography (Riedl, S.J., Li, W., Chao, Y., Schwarzenbacher,
R., Shi, Y. Structure of the apoptotic protease-activating factor 1 bound to ADP Nature v434 pp.926933 , 2005), and deposited in the PDB under the accession number 1Z6T.
Image 1: the NBS domain
Apaf1 crystallized as a tetramer. Each monomer contains 3 main domains: the CARD domain, the NBS
domain, and a helical domain II. Here we focus on the NBS domain, which includes all residues between
125 and 449. The NBS domain can itself be divided into 3 sub-domains: a  fold (residues 125 to
284), the helical domain I (residues 285 to 365) and a winged helix domain (residues 366 to 449).
 fold
Winged
helix domain
Helical
domain I
Part 2: The ADP binding domain:
Apaf1 binding
Ploop
Kinase-2
D244
R129
Anchor
V127
K160
D243
H438
ADP
S422
Winged helix Domain
Information about hydrogen bonding in this molecule that was used to generate the above image.
(Code for displaying these specific hydrogen bonds is in handout “Pymol Hints”):
ADP binds to the NBS domain of Apaf1 making contacts with 4 main regions:
- the “Anchor” region, from residue 125 to 131
- the “Ploop” region, from residue 160 to 164
- two regions in the winged helix domain: from residues 420 to 424 and from 436 to
440
- the “Kinase-2” region, from residue 241 to 245
The specific interacting residues are: V127, R129, K160, D243, D244, H438 and S422.
There are 8 specific hydrogen bonds between Afap1 and ADP:
1z6t, residue 127, atom N to ADP, atom N1
1z6t, residue 127, atom O to ADP, atom N6
1z6t, residue 159, atom N to ADP, atom O2B
1z6t, residue 160, atom N to ADP, atom O2B
1z6t, residue 160, atom NZ to ADP, atom O2B
1z6t, residue 161, atom N to ADP, atom O1B
1z6t, residue 162, atom N to ADP, atom O1A
1z6t, residue 438, atom NE2 to ADP, atom O3B
(Note that for simplicity, the hydrogen atoms are omitted, and replaced with the heavy atom they
are attached to).