+Open data
-Basic information
Entry | Database: PDB / ID: 5aph | ||||||
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Title | Ligand complex of RORg LBD | ||||||
Components |
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Keywords | TRANSCRIPTION / RORG LIGAND / RORG AGONIST / STRUCTURE-BASED DESIGN | ||||||
Function / homology | Function and homology information ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / lymph node development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / adipose tissue development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / transcription regulator complex / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Xue, Y. / Aagaard, A. / Narjes, F. | ||||||
Citation | Journal: ChemMedChem / Year: 2016 Title: Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor ROR gamma. Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. ...Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. / Hansson, T.G. / Narjes, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aph.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aph.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 5aph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/5aph ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5aph | HTTPS FTP |
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-Related structure data
Related structure data | 5apjC 5apkC 3l0lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30901.402 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 265-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51449 |
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#2: Protein/peptide | Mass: 1492.788 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 686-697 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E7EWM1, UniProt: Q15596*PLUS |
#3: Chemical | ChemComp-VYI / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | N-(2-FLUOROPHENYL)-4-[(4-FLUOROPHENYL)SULFONYL]-2,3,4, 5-TETRAHYDRO-1,4-BENZOXAZEPIN-6-AMINE (VYI): ...N-(2-FLUOROPHEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→48.82 Å / Num. obs: 43870 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 30.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.54→1.59 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.3 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L0L Resolution: 1.54→48.82 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.9268 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.091
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Displacement parameters | Biso mean: 33.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→48.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20
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