A wiki that has lots of information about proteins. It is a great place to start learning about a protein. It works somewhat like Wikipedia, except that not all the pages are open for general editing and the pages are edited by people knowlegeable about proteins.
Protein Data Bank
The Protein Data Bank (PDB) is a repository for all solved protein structures. It gives coordinates for all atoms and other information about the protein structure.
A database maintained by the National Institutes of Health (NIH) which tries to organize all the information available about biomedical sciences. It links together sequences, structures, references, etc
Structural Classification of Proteins (SCOP) organizes proteins into families based on their structural similarities.
Kyoto Encyclopedia of Genes and Genomes is a database of the metabolic pathways in different organims. It neatly displays these pathways and the enzymes and metabolites involved in them. It is easiest to use if you enter an EC number for a particular enzyme. To do this, choose SEARCH OBJECTS IN KEGG PATHWAYS from the top table. Enter your EC number and click Exec.
OMIM is a catalog of human genes and genetic disorders. It is easiest to use if you enter an EC number for a particular enzyme.
A list of more than 2700 natural and synthetic small molecular entities: atoms, molecules, free radicals, ions, and other chemicals with biological impact. It lists the substance's chemical classification, function, alternate names, structure, a link to KEGG, and the proteins it interacts with.