This is a spacefill diagram showing a hydrophobic pocket in yellow, oxygen in red, nitrogen in blue and carbon in grey. A haem group has been made transparent. I think this looks damn fine. Above is a diagram of a wir plot. Alpha helices can be seen at H1 to H5.
Red lines represent the anti-parallel beta sheets looping around themselves.
Purple arrows are beta strands. The 2 diagrams below are of the molecule Phosphoenolpyruvate Carboxykinase from the organism E. Coli. The pink swirls in the above picture represent alpha helices, and the yellow strands represent b-pleated sheets. This diagram clearly shows the ligand component of the protein. Consisting of an ATP and OXL molecule, and a Magnesium atom displayed in green.