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The <scene name='48/483885/Alphabeta_picture/1'>vitamin d receptor</scene> contains 427 amino acids with a total molecular weight of 48,289 Da. The protein is also composed almost entirely of alpha helices with only a single beta sheet. The vitamin D receptor also does not have a quaternary structure [2]. Vitamin D3 is a large organic compounds made up of 27 carbon atoms, 44 hydrogen atoms and a single oxygen atom, with the ligand having a total molecular weight of 385 Da [3]. <br><br> | The <scene name='48/483885/Alphabeta_picture/1'>vitamin d receptor</scene> contains 427 amino acids with a total molecular weight of 48,289 Da. The protein is also composed almost entirely of alpha helices with only a single beta sheet. The vitamin D receptor also does not have a quaternary structure [2]. Vitamin D3 is a large organic compounds made up of 27 carbon atoms, 44 hydrogen atoms and a single oxygen atom, with the ligand having a total molecular weight of 385 Da [3]. <br><br> | ||
Other aspects of interest about the vitamin D receptor include the protein revealing a binding pocket when it is in its active folded state, allowing the ligand to bind to the receptor. The ligand interacts with the activation helix by stabilizing the agonist position. This is accomplished through Van der Waals interactions between the ligand and the activation helix. The activation ligand is a nuclear receptor. There is also some empty space observed around the aliphatic chain [1]. | Other aspects of interest about the vitamin D receptor include the protein revealing a binding pocket when it is in its active folded state, allowing the ligand to bind to the receptor. The ligand interacts with the activation helix by stabilizing the agonist position. This is accomplished through Van der Waals interactions between the ligand and the activation helix. The activation ligand is a nuclear receptor. There is also some empty space observed around the aliphatic chain [1]. | ||
The protein has an active conformation of 1,25 (OH)_2D_3 that has a ligand binding pocket in its active folded state. The activation ligand, a nuclear receptor (VDR), interacts with with the activation helix by stabilizing the agonist position. This is accomplished through Van der Waals interactions between the ligand and the activation helix. There is some empty space observed around the aliphatic chain, indicating the presence of water to stabilize all possible hydrogen bonds [1]. | |||
==Binding Interactions== | ==Binding Interactions== | ||
Protein 1db1 is found to complex with 1,25 Dihydroxy <scene name='48/483885/Vitamin_d3/1'>Vitamin D3</scene>. This molecule has three notable alcohol groups shown in red. Oxygen is electronegative, giving alcohols the ability to participate in hydrogen bonding with the protein. Vitamin D3 has a large number of relations with the residues on the protein chain. First in the sequence are <scene name='48/483885/Residues_140-151/2'>residues 140-151</scene>. Tyr143, shown in blue, is the closest to the ligand at 2.83 angstroms. This is sightly large but there is still the possibility of hydrogen bonding. Tyr147 in green and Phe150 in black are also known to have interactions with Vitamin D3 they are farther away and therefore less significant. Next down the peptide chain are <scene name='48/483885/Residues_235-240/1'>residues 235-240</scene>. Ser237, shown in green, has significant interactions with vitamin D3 this can be seen by its short distance 2.78 angstroms. Only 40 residues away, more hydrogen bonding is occurring.<scene name='48/483885/Residues_270-280/1'>Arg274 and Ser278</scene> form bonds with the same oxygen atoms as Tyr143 and Ser237 respectively. This means that the oxygen atoms of vitamin D3, when bound to the receptor, are negatively charged and stabilized by protons. On the opposite end of vitamin D3 there is an additional negatively charged oxygen. Although this oxygen does not participate in hydrogen bonding. <scene name='48/483885/His305_and_his397/1'>His305 and His397</scene>, shown in blue and green respectively, Contain aromatic rings. These rings are able to momentarily accept the electrons donated by the oxygen because they can delocalize the charge. This creates two pseudo-covalent bonds that is approximately 2.81 angstroms. When looking at <scene name='48/483885/All_binding_interactions/1'>all binding interactions</scene>, it can be seen that all of the binding sights are centered around oxygen | Protein 1db1 is found to complex with 1,25 Dihydroxy <scene name='48/483885/Vitamin_d3/1'>Vitamin D3</scene>. This molecule has three notable alcohol groups shown in red. Oxygen is electronegative, giving alcohols the ability to participate in hydrogen bonding with the protein. Vitamin D3 has a large number of relations with the residues on the protein chain. First in the sequence are <scene name='48/483885/Residues_140-151/2'>residues 140-151</scene>. Tyr143, shown in blue, is the closest to the ligand at 2.83 angstroms. This is sightly large but there is still the possibility of hydrogen bonding. Tyr147 in green and Phe150 in black are also known to have interactions with Vitamin D3 they are farther away and therefore less significant. Next down the peptide chain are <scene name='48/483885/Residues_235-240/1'>residues 235-240</scene>. Ser237, shown in green, has significant interactions with vitamin D3 this can be seen by its short distance 2.78 angstroms. Only 40 residues away, more hydrogen bonding is occurring.<scene name='48/483885/Residues_270-280/1'>Arg274 and Ser278</scene> form bonds with the same oxygen atoms as Tyr143 and Ser237 respectively. This means that the oxygen atoms of vitamin D3, when bound to the receptor, are negatively charged and stabilized by protons. On the opposite end of vitamin D3 there is an additional negatively charged oxygen. Although this oxygen does not participate in hydrogen bonding. <scene name='48/483885/His305_and_his397/1'>His305 and His397</scene>, shown in blue and green respectively, Contain aromatic rings. These rings are able to momentarily accept the electrons donated by the oxygen because they can delocalize the charge. This creates two pseudo-covalent bonds that is approximately 2.81 angstroms. When looking at <scene name='48/483885/All_binding_interactions/1'>all binding interactions</scene>, it can be seen that all of the binding sights are centered around oxygen | ||