With[{p="CD2AP",cr=Dispatch@ColorData["Atoms","ColorRules"]},Graphics3D[MapThread[{#2/.cr,Sphere[#1,QuantityMagnitude@ElementData[#2,"AtomicRadius"]]}&,{QuantityMagnitude@ProteinData[p,"AtomPositions"],Flatten[ProteinData[p,"AtomTypes"]]}],Boxed->False]
]