Protein Structure for PDB 3U8V
by MoleculeMaker, published
This is my second attempt to print out a protein structure based on a pdb file. This printed well, and is now a completed model. I am planning to paint it soon, and will post more later.
This protein is a simple protein with a series of 7 amino acid repeat motifs, highlighted by a histidine residue. The crystal structure revealed that these histidines form a 4 alpha helical bundle, and the histidines seem to form a zipper pattern. I built the model with these histidine residues displayed. This is a natural protein, found in the organism Nitrosomonas europaea, which is commonly found in wastewater treatment plants.
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This structure is an extensive print. THIS CAN ONLY BE PRINTED WITH BOTH RAFT AND SUPPORT selected, and a word of warning, expect 5-6 hours to remove the support and get down to the actual model. I removed the supports as well, and am preparing to paint.. I am printing at medium quality. The build time was nearly 15 hours, so be warned, it takes some time. Also had some issues with the raft separating from the build plate, but with the supports included, this didn't seem to matter. I printed this out on a Makerbot Replicator 2.
The model took a good deal of effort to construct. The original pdb file (3U8V) was manipulated until only a single dimer 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 residues for display as CPK, and added some bonds to serve as supports to hold the structure together (these are the larger braces). 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.
If you do choose to print this out, be prepared for a significant level of work, but the print is very nice.