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4

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 ...


3

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be ...


2

There are no MTRIX cards for that molecule. This seems like the easiest path: http://www.rcsb.org/pdb/explore.do?structureId=4G3Y Download Files -> Biological Assembly 1 i.e.: http://www.rcsb.org/pdb/files/4G3Y.pdb1.gz And read that file into Coot (should you wish)


2

The residue numbering convention in the PDB is more-or-less entirely up to the depositor of the structure. While generally speaking sequential numbers are next to each other, there is no guarantee of that fact. For example, the PDB allows for what are called "insertion codes", which are extra residues which interrupt the regular sequence progression. For ...


2

This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need some experimental data on the structure of your proteins. If your proteins have not been structure ...


1

The PDB-file only contains the asymmetric unit, and no information on a potential biological relevant multimer. So you will need to get information about the state in solution experimentally. That being said, one can often deduce from the size of the contact surface whether you have a potential quarternary structure. You can do this by hand, but the PISA-...


1

I know the question is old, but for the record: the RCSB PDB is currently working on a project to compress the PDB structural data with a new file format, called MMTF (MacroMolecular Transmission Format). The format uses MessagePack for serialization and does custom compression, achieving ~ 5x advantage over mmCIF gzipped files. Currently the whole PDB ...



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