- PDB-3auq: Crystal structure of the human vitamin D receptor ligand binding ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3auq
Title
Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2alpha-methyl-19-norvitamin D3
Components
Vitamin D3 receptor
Keywords
TRANSCRIPTION / HORMONE RECEPTOR
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 / lithocholic acid 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 / lithocholic acid binding / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / 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 / Nuclear Receptor transcription pathway / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / 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: 2.64→42.03 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.687 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 1.197 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28639
442
4.8 %
RANDOM
Rwork
0.23446
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-
-
obs
0.23697
8816
97.09 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 42.815 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.64→42.03 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2018
0
30
10
2058
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
2090
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.024
2.003
2832
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.469
5
251
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.485
24.286
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.222
15
383
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.879
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.062
0.2
328
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
1535
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.169
0.2
986
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.291
0.2
1463
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.093
0.2
57
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.163
0.2
32
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.101
0.2
3
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.305
1.5
1316
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.546
2
2065
X-RAY DIFFRACTION
r_scbond_it
0.438
3
863
X-RAY DIFFRACTION
r_scangle_it
0.761
4.5
767
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.64→2.708 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.351
27
-
Rwork
0.266
625
-
obs
-
-
96.59 %
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