There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB incorporate the SNP's into their structure? If not, is there a way to visualize protein structure using any tool after a SNP on the protein? I know that tools like SIFT exist but they only say whether or not a SNP is harmful or not. They don't comment on the structure of the protein in anyway.
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 trying to get the 3D structure if an SNP leads to a frameshift or an early stop codon.
What you can do is simply load the PDB structure of the wildtype protein into a viewer like PyMol and look at the amino acid that is changes by the SNP. Read the associated paper to find out if that residue is important in some way. This won't be always possible, but if e.g. the amino acid is in the catalytic center of an enzyme, this would explain how the SNP affect the function of 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)