New answers tagged structural-biology
501 denotes 501st residue in the corresponding PDB entry — 1BDG. See here A single protein can have multiple cavities (see here) and the multiple entries denote centres of different cavities.
That depends on what your are trying to do. Apparently your query sequence is similar to that of proteins with a known 3D-structure. As it says on Jpred's result page (and help), in this case it might be worth looking at these homologues with experimentally determined structures for information on secondary structure. Most likely it will be more accurate ...
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