User:Adam Davis/Sandbox 1: Difference between revisions

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== Structural highlights ==
== Structural highlights ==


This is an X-ray crystallography structure, solved at 1.95 Å, which models the region of PPARδ from Gln171 to Tyr441<ref>DOI 10.1371/journal.pone.0033643</ref>. It is composed of <scene name='10/1079455/Helices/1'>twelve alpha helices</scene>, with one small <scene name='10/1079455/Beta_sheet/1'>beta sheet region</scene>. The structure is bound to a synthetic ligand, <scene name='10/1079455/Ligand/2'>GW0742</scene>, which contains a carboxylate group, a thiophenol, a thiazole, and a fluorine substituted phenyl ring. This ligand can be divided into a hydrophilic head group (carboxylate) and a hydrophobic tail (thiophenol, thiazole, phenyl). There is also a glycerol molecule in the structure, which is an artifact of the crystallization process and is not biologically relevant.   
This is an X-ray crystallography structure, with a resolution of 1.95 Å, which models the region of PPARδ from Gln171 to Tyr441<ref>DOI 10.1371/journal.pone.0033643</ref>. It is composed of <scene name='10/1079455/Helices/1'>twelve alpha helices</scene>, with one small <scene name='10/1079455/Beta_sheet/1'>beta sheet region</scene>. The structure is bound to a synthetic ligand, <scene name='10/1079455/Ligand/2'>GW0742</scene>, which contains a carboxylate group, a thiophenol, a thiazole, and a fluorine substituted phenyl ring. This ligand can be divided into a hydrophilic head group (carboxylate) and a hydrophobic tail (thiophenol, thiazole, phenyl). There is also a glycerol molecule in the structure, which is an artifact of the crystallization process and is not biologically relevant.   


The ligand binding pocket (LBP) is made of <scene name='10/1079455/Armsi_ii_iii/2'>three arms</scene> (Arm I residues are green, Arm II residues are blue, Arm III residues are red), with fifteen residues that contact the ligand. <scene name='10/1079455/Armi/1'>Arm I</scene> interacts with the ligand through Phe246, Cys249, His287, Phe291, Ile327, His413, Leu433, and Tyr437. The <scene name='10/1079455/Hydrophilic_head/2'>hydrophilic head</scene> of the ligand interacts via polar contacts with Arm I residues His287, His413, and Tyr437. <scene name='10/1079455/Arm_ii/1'>Arm II</scene>, includes residues Val245, Val305, Val312, Leu317, and Ile 328, while <scene name='10/1079455/Arm_iii/1'>Arm III</scene> includes Leu249 and Thr252. The <scene name='10/1079455/Hydrophobic_tail/2'>hydrophobic tail</scene> of the ligand interacts via nonpolar contacts with residues from all three arms (Phe246, Phe291, His 413, Ile327, Leu433, Cys249, Val245, Val305, Val312, Leu317, Ile328, Thr252, and Leu294).  
The ligand binding pocket (LBP) is made of <scene name='10/1079455/Armsi_ii_iii/2'>three arms</scene> (Arm I residues are green, Arm II residues are blue, Arm III residues are red), with fifteen residues that contact the ligand. <scene name='10/1079455/Armi/1'>Arm I</scene> interacts with the ligand through Phe246, Cys249, His287, Phe291, Ile327, His413, Leu433, and Tyr437. The <scene name='10/1079455/Hydrophilic_head/2'>hydrophilic head</scene> of the ligand interacts via polar contacts with Arm I residues His287, His413, and Tyr437. <scene name='10/1079455/Arm_ii/1'>Arm II</scene>, includes residues Val245, Val305, Val312, Leu317, and Ile 328, while <scene name='10/1079455/Arm_iii/1'>Arm III</scene> includes Leu249 and Thr252. The <scene name='10/1079455/Hydrophobic_tail/2'>hydrophobic tail</scene> of the ligand interacts via nonpolar contacts with residues from all three arms (Phe246, Phe291, His 413, Ile327, Leu433, Cys249, Val245, Val305, Val312, Leu317, Ile328, Thr252, and Leu294).  
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