Hot answers tagged pdb
Swiss PDB Viewer allows you to mutate residues in an existing structure and explore the effects. I'm pretty sure that UCSF Chimera does too.
Solving the 3D structure of a protein is hard and a lot of work, doing that for every common SNP of a protein would be excessive in most cases. So you generally won't find such structures unless the structure of the specific mutated version is particularly interesting. In many cases it is also not structurally interesting what happens, there is no point in ...
You saw my last answer of your question? you can do that easily, just use prepare_ligand4.py -l my.mol2 -A "hydrogens"
You may consider taking a look at the SCOP structural classification of proteins to check all beta proteins and all alpha proteins. As per specific examples and though not belonging to the SCOP classes mentioned above, Porin for a beta protein (PDB:1A0S), and Rhodopsin for an alpha protein (PDB:1F88) are two nice structures to look at.
The pdb file that you mention is entitled: V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose). So, it isn't a protein at all, it is a circular oligosaccharide consisting of 26 glucose (GLC) residues. I imagine that the usual fields in the pdb file have been fudged to accommodate this.
None of them is integrase: P12497 Protein Gag-Pol polyprotein Gene gag-pol Organism Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1) P14350 Protein Pro-Pol polyprotein Gene pol Organism Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus) Even if you meant the integrase product of the polyprotein, the ...
The number of hydrogen bonds cannot actually be said from software only inferred. But you could try using STRIDE (http://structure.usc.edu/stride/) which takes the file name with a -h flag to output the number of hydrogen bonds. You could then write a small shell script which would pass in each file and store the data you wanted in whatever format you liked. ...
Here a solution that does not require you to upload the files to the servers: You can graphically visualize DSSP and Stride at the Sequence Page at RCSB PDB: http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&bionumber=1 "add annotation" -> Stride and look at the graphical comparison between DSSP and Stride.
You can find examples by using the "drilldown" function at the RCSB PDB homepage: Click on the number 103921 at the top of the page at http://www.rcsb.org then find the "SCOP Classification" section and then e.g. select "All alpha proteins".
Here's one: http://www.rcsb.org/pdb/explore/explore.do?structureId=2IPH. It was crystallized with the inhibitor bound to the protein.
check out the sequence page at RCSB PDB, it can show SNPs mapped onto 3D for some of the proteins (you need to enable the SNP annotations in the drop-down) http://www.rcsb.org/pdb/explore/remediatedSequence.do?params.showJmol=true&structureId=4HHB
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