Cover: A montage of images from the PDBsum web server (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum). Most come from the entry for PDB code 1nn3 which is the crystal structure of human thymidylate kinase complexed with two magnesium ions and two small molecules: 3'-deoxythymidine-5'-monophosphate (dTMP) and adenosine-5'-diphosphate (ADP). The central picture shows the surface of the protein, with the most highly conserved residues coloured red and the remainder coloured white, plus the two small molecule ligands shown in yellow spacefill and one of the two magnesium ions visible as a green sphere. The other pictures, starting to the right of the central image and going clockwise, are: a LIGPLOT diagram giving a "flattened" schematic representation of the interactions that the bound ATP makes with the protein residues and metal ion; a diagram of the protein's secondary structure motifs mapped onto its sequence; a picture of the 3D conformation of the ATP molecule; a miniature Ramachandran plot for one of the protein's beta turns (a type II turn involving residues 121 to 124); a schematic picture of the contents of entry 1nn3 with the protein shown in purple, its helices as cylinders and strands as arrows, and the ligands and metals shown in spacefill; and finally a Ramachandran plot showing the phi-psi main chain torsion angles of all the protein's residues. Other images in the montage include some of the creatures from the PDBsum Species analysis, the 3-sphere Rasmol icon, the PDBsum logo, and the logos of two closely related servers: EC
PDB (the Enzyme Structures Database), and SAS (Sequences Annotated by Structure).
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