pdbBAM is a binary sequence alignment/mapping (BAM) formatted file, in which proteins in Protein Data Bank (PDB) are represented in their positions of the human genome. The amino acid sequences of PDB proteins are first transformed to mRNA sequences and their location in the human genome are identified together with their exon-intron structures. Not only human proteins in PDB but also those proteins in PDB that are similar in sequence to the human proteins are included in pdbBAM, so that its coverage in human genes is extended. Structural information of such homologous/similar proteins can be useful in inferring the structural and funtional importance of those proteins whose 3D structure is not yet solved.