Cytochrome C (Human) (PDB 1J3S)
by MoleculeMaker, published
This is a model of the structure of human cytochrome C. The model is based on the solution structure and the PDB file 1J3S.
This printed well, and is now a completed model. I have painted it and provided some pictures.
This protein is the human version, and is important for the transfer of electrons in the electron transport chain. It has a single heme heteroatom, which I have represented as CPK, along with the histidine ligand. I was a little bit upset by how flimsy it was following the initial print, but actually have grown to like it very much, as it gives one the sense of the fluidity of the protein backbone and structure. It is not as sturdy as some of my other models, but turned out very nice.
This structure is an extensive print. THIS CAN ONLY BE PRINTED WITH SUPPORT selected in Makerware, and a word of warning, expect 2-3 hours to remove the support and get down to the actual model. I removed the supports as well, and have painted it. I am printing at medium quality. The build time was nearly 8 hours, so be warned, it takes some time. This model is somewhat fragile, so take your time removing the support. I use a pair of needlenose pliars to break off the support structure slowly, and remove the support from the remaining model. I printed this out on a Makerbot Replicator 2.
The model took a good deal of effort to construct. The original pdb file (1J3S) was manipulated until only the single monomer with no water molecules was included. This was then placed into the program VMD. I manipulated the backbond as cartoons, and then selected the histidine ligand and heme for display as CPK, and added some bonds to serve as supports to hold the structure together (these are somewhat flimsy). This was then imported in several segments into tinkercad (tinkercad had a problem importing files larger than 20 Mb, so I had to import and then align as three components. I then grouped and aligned everything, and added a number of manual support features at the bottom. The smaller braces are designed to be removed, while the larger braces hold the model together. I did break a small section at the end of the molecule at one point, which I had to glue along with one of the supports for the heme. These glued well with standard model glue.
If you do choose to print this out, be prepared for a significant level of work, and be patient removing the supports, but the print is very nice. I painted the alpha helices in orange and the beta sheets in teal, and also painted the individual atoms of the heme and histidine ligand. The iron was painted green.