- PDB-3s9s: Ligand binding domain of PPARgamma complexed with a benzimidazole... -
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Basic information
Entry
Database: PDB / ID: 3s9s
Title
Ligand binding domain of PPARgamma complexed with a benzimidazole partial agonist
Components
Nuclear receptor coactivator 1
Peroxisome proliferator-activated receptor gamma
Keywords
TRANSCRIPTION / PPAR / NUCLEAR RECEPTOR
Function / homology
Function and homology information
labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Complex I biogenesis / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Respiratory electron transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / mitochondrial ATP synthesis coupled electron transport / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / mitochondrial respiratory chain complex I assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / protein dimerization activity / mitochondrial inner membrane / positive regulation of apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function
Resolution: 2.55→61.3 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 28.847 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.284
477
4.8 %
RANDOM
Rwork
0.224
-
-
-
obs
0.227
9418
95.9 %
-
all
-
9418
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 71.789 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.9 Å2
0 Å2
0 Å2
2-
-
1.41 Å2
0 Å2
3-
-
-
-3.31 Å2
Refinement step
Cycle: LAST / Resolution: 2.55→61.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2095
0
31
52
2178
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
2174
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.158
2.006
2939
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.678
5
263
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.597
24.831
89
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.841
15
387
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.106
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
344
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
1653
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
0.379
1.5
1334
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.709
2
2143
X-RAY DIFFRACTION
r_scbond_it
1.102
3
840
X-RAY DIFFRACTION
r_scangle_it
1.799
4.5
796
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.55→2.62 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.436
32
-
Rwork
0.313
614
-
obs
-
-
85.22 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.7054
0.362
0.029
4.039
1.2138
4.1737
-0.3234
0.3298
-0.0313
-0.7163
0.4927
-0.223
0.2007
0.3127
-0.1692
0.2732
-0.1563
0.0374
0.4686
-0.0271
0.2901
-22.984
11.502
-14.795
2
31.4269
5.5352
-0.7349
38.0571
-3.7434
8.5971
-1.1523
2.2528
-1.1826
-2.2688
1.0214
-1.4601
0.6558
2.4691
0.1309
0.3262
-0.2305
0.1945
1.5004
-0.2658
0.6484
-3.396
14.013
-14.06
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
208 - 476
2
X-RAY DIFFRACTION
2
B
686 - 695
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