Final answer:
To verify the sequence similarity between your cDNA cloned protein and a protein structure, download the PDB file from the RCSB Protein Data Bank and use BLAST to compare the sequences.
Step-by-step explanation:
The best way to verify the sequence similarity between the protein determined from your cDNA clone and the protein in a crystal structure is to use the RCSB Protein Data Bank.
Initially, you need to download the PDB file associated with the protein structure you're interested in, which has a unique identification code. Once you have the structural data, the next step is to compare the amino acid sequence found in the PDB file with your sequence using a tool like BLAST (basic local alignment search tool).
BLAST facilitates the comparison of very protein sequences against protein sequences extracted from PDB 3-dimensional structure records. This allows you to determine the percentage of conservation and trends in the types of amino acids that are conserved. To complete this analysis, you can use the sequence alignment to identify any functional or structural conservation that may exist between the PDB protein and your cDNA clone sequence.