Hot answers tagged pdb
With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).
ProDy works quite well, especially from within an existing Python script. The following code takes an existing PDB file, performs some selection query on it, then saves it to another file. import prody def pdbsubset(inpdb, outpdb, selection): with open(inpdb) as protf: prot = prody.parsePDBStream(protf) atoms = prot.select(selection) ...
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 are making a few assumptions that are likely not valid for all PDB files. For example: Residue indices are not necessarily sequential, nor do they have to start at 1 Not all possible residues have 1-letter code equivalents, there are thousands of possible exotic residues, not only the standard amino acids PDB files are not only used for proteins, but ...
There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised. Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed ...
Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)
The PDB file format was specified in the dawn of computing to fit on punch cards. So it has some shortcomings that have led to generations of scientists cursing the fixed-width column format. By now, it has been superseded by an XML-like format: PDBML. Of course XML is less space-efficient than a column layout, so you can see that disk space was not the main ...
These two links go through the specifications required for the PDB format: Link1: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look ...
PDB residues are described by the residue number and an insertion code. Residue numbers can be any number, including negative values. In 3CKR the first residue has nr. -6, followed by -5, etc. This might indicate that there are additional residues at the beginning of the sequence, relative to other PDB entries. In 2P83, the first residue has the number 61P. ...
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
only a small peptide of Osteopontin is available currently http://www.rcsb.org/pdb/protein/P10451
As pointed out in the comments, if you look for PDB files and you don't find them in the PDB, there is no solved structure. However, you can look in databases that contain models of proteins. Especially for the receptors the coverage has been increasing in recent years and so you may be lucky. A good starting place to look for protein information is ...
This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined. shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP ...
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