Sandbox Reserved 960: Difference between revisions
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=== Cavity === | === Cavity === | ||
The dynamic structure of the protein is responsible of the ligand’s binding by adjustment of position. The successful delivery of the effector to the receptor relies on this property. The ligand binding pocket consists in a <scene name='60/604479/Cavity/ | The dynamic structure of the protein is responsible of the ligand’s binding by adjustment of position. The successful delivery of the effector to the receptor relies on this property. The ligand binding pocket consists in a <scene name='60/604479/Cavity/3'>cavity</scene> formed by the helices H2, H4 and H5 (scene), arranged in a globular shape which leads to a clear separation of the ligand from the {{Template:ColorKey_Polar}} environment. | ||
The top of the cavity is not closed and can establish contacts with the solvent. The cavity is prone to accept ligand such as 9-ODA because of its specific composition. Indeed, cavity's components are mainly <scene name='60/604479/hydrophobic_residues/2'>hydrophobic and aromatic</scene> <ref>PMID: 14594955</ref>.They consequently interact with the ligand's {{Template:ColorKey_Hydrophobic}} carbon chain and are localized on the internal face of the helix.Thus, it implies that these residues respect a regular distance pattern in the primary structure of the AmelASP1. | The top of the cavity is not closed and can establish contacts with the solvent. The cavity is prone to accept ligand such as 9-ODA because of its specific composition. Indeed, cavity's components are mainly <scene name='60/604479/hydrophobic_residues/2'>hydrophobic and aromatic</scene> <ref>PMID: 14594955</ref>.They consequently interact with the ligand's {{Template:ColorKey_Hydrophobic}} carbon chain and are localized on the internal face of the helix.Thus, it implies that these residues respect a regular distance pattern in the primary structure of the AmelASP1. | ||
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*[[Image:GOL_Ligplot.png|200px|left|thumb|'''Fig.3''' GOL Ligplot]]<scene name='60/604479/Gol/1'>Glycerol</scene> (C3H8O3) also known as GOL, is a ligand used for cryoprotection during the purification process of the protein. It is supposedly helping the main ligand to reach its binding site. | *[[Image:GOL_Ligplot.png|200px|left|thumb|'''Fig.3''' GOL Ligplot]]<scene name='60/604479/Gol/1'>Glycerol</scene> (C3H8O3) also known as GOL, is a ligand used for cryoprotection during the purification process of the protein. It is supposedly helping the main ligand to reach its binding site. | ||
To do so, GOL links to<scene name='60/604479/Gol_binding_residues/1'> Asn 41 and Tyr 102.</scene> | To do so, GOL links to<scene name='60/604479/Gol_binding_residues/1'> Asn 41 and Tyr 102.</scene> | ||
[[Image:Cl_Ligplot.png|right|thumb|'''Fig.4''' Cl Ligplot]] | [[Image:Cl_Ligplot.png|right|thumb|'''Fig.4''' Cl Ligplot]] | ||
