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4

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.


2

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.


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In babel: babel my.mol2 my.pdbqt -xh -x states options for writing .pdbqt files -h says keep hydrogens


1

The "chain identifier" does exactly what it says: it identifies the polypeptide or other molecular chain. For some structures, there is only one, so you'll only see an identifier A. However, many structures show two or more proteins bound together, or an enzyme complexed to a substrate, or a small molecule inhibitor in a binding pocket - there are many ...


1

This is actually a very difficult problem, because a given compound may exist in multiple conformations (have multiple structures), and it might not be obvious what conformation is most relevant. For example, a seemingly simple compound like glucose has multiple stereoisomers: if you say "glucose", you probably mean alpha-D-glucose, as opposed to ...


1

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 ...


1

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. ...


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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.


1

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".



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