Chapter 3 - Crystallographic Coordinates and Stereodrawings

Abstract

The chapter provides information on the Protein Data Bank (PDB) file. In early 1999, 9236 sets of protein coordinates became available through a structural biology database called the PDB. It is customary for investigators to send the crystal or solution coordinates to the PDB upon completion of a structural study of a crystalline protein. In a PDB file, the syntax and arrangement of the atom coordinates should be comprehensible. The chapter describes the information provided in such files. It provides requisite information on the data depending on the crystallographic or NMR method used. The chapter discusses header records for PDB files, coordinates, atom records in a PDB file, and atom labels along with other contents of the PDB files— such as, stereodrawings, stereoglasses, divergent eyes, crossed eyes, and amino acids. The chapter focuses on the method of viewing protein models in a computer, and describes the four letter identification code. The chapter also provides guidelines on downloading coordinates with File Transfer Protocol (FTP), and using the World Wide Web page for PDB. The how-to for displaying PDB coordinates is provided, and finally the PREKIN and MAGE program is described in detail in the chapter.