Sandbox 47: Difference between revisions
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Adenylate kinase has multiple units of <scene name='Sandbox_47/Adenylate_kinase_secondary/1'>Secondary Structure</scene>, including alpha helices (blue) and beta sheets (red). The protein structure is held together with <scene name='Sandbox_47/Ade_kin__secondary_hbond/1'>hydrogen bonds</scene> (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids. | Adenylate kinase has multiple units of <scene name='Sandbox_47/Adenylate_kinase_secondary/1'>Secondary Structure</scene>, including alpha helices (blue) and beta sheets (red). The protein structure is held together with <scene name='Sandbox_47/Ade_kin__secondary_hbond/1'>hydrogen bonds</scene> (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids. | ||
The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>polar residues</scene> are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> allows one to see the general patterns of arrangement relative to each other. | The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> (gray) of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>polar residues</scene> are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> allows one to see the general patterns of arrangement relative to each other. | ||
The hydrophillic residues often find themselves in interactions with the <scene name='Sandbox_47/Adenylate_kinase_water/1'>water</scene> | The hydrophillic residues often find themselves in interactions with the <scene name='Sandbox_47/Adenylate_kinase_water/1'>water</scene> | ||
