- PDB-5ysy: Crystal structure of the human vitamin D receptor ligand binding ... -
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Basic information
Entry
Database: PDB / ID: 5ysy
Title
Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
Components
Vitamin D3 receptor
Keywords
TRANSCRIPTION / Active ligand / Complex
Function / homology
Function and homology information
regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / bile acid signaling pathway / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / calcium ion transport / nuclear receptor activity / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function
Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.58 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.165 Details: 1. The authors state they removed the long loop 165-215 for the crystallization with direct lincage with Gly 164 and Ser 216, so this region recieved quite large steric hindrance and resuled ...Details: 1. The authors state they removed the long loop 165-215 for the crystallization with direct lincage with Gly 164 and Ser 216, so this region recieved quite large steric hindrance and resuled abnormal bond length as usual, and that the bond is existing in real but the bond distance is abnormal by the disorder by the steric hindrances. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24223
1097
5.1 %
RANDOM
Rwork
0.18936
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obs
0.19196
20302
99.93 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å