Homology modeling will try to model the regions of your protein that are similar in sequence to other proteins of known structure in a given database. It is possible that certain regions of your protein will not be modeled. That being said you can check at:
if your protein is not there try using http://swissmodel.expasy.org/ This tool will get your query protein sequence and try to find templates that exist in their database.
There are also other automated servers such as I-TASSER: http://zhanglab.ccmb.med.umich.edu/I-TASSER/
You can either use native I-TASSER algorithm which takes into account existing templates or the QUARK: http://zhanglab.ccmb.med.umich.edu/QUARK/ which does ab initio prediction, meaning from scratch, without templates and only taking into account the amino acid sequence.
You can also try the automated PHYRE2 server: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
Here you will have 2 modes, normal and intensive. Templates are used here as well. For all residues you will get a key of confidence scores giving you an idea about the reliability of the model/region that is modeled.
All these are some guidelines. The aforementioned websites will send you results within 1-4 days, no additional work needed other than submitting your fasta sequence. The resulting models should be interpreted carefully, trying to take into account proteins with similar function/structure with known 3D confimation where possible,
I hope this helps,
Good luck with your research,
Further to Ibrahim's reply:
If your protein sequence is in UniProtKB, you can have a look at the "Structure" section of the entry, which links to various model databases, even if no cross-references to PDB are available, e.g. ProteinModelPortal, SMR (Swiss-Model repository), ModBase and MobiDB, e.g. http://www.uniprot.org/uniprot/Q96J66#structure