+Open data
-Basic information
Entry | Database: PDB / ID: 5apk | ||||||
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Title | Ligand complex of RORg LBD | ||||||
Components | (NUCLEAR RECEPTOR ROR-GAMMA) x 2 | ||||||
Keywords | TRANSCRIPTION / RORG LIGAND / RORG AGONIST / STRUCTURE-BASED DESIGN | ||||||
Function / homology | Function and homology information T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 5apk.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5apk.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 5apk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/5apk ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5apk | HTTPS FTP |
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-Related structure data
Related structure data | 5aphC 5apjC 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: 30918.490 Da / Num. of mol.: 2 / 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 #2: Protein/peptide | | Mass: 1632.925 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 480-492 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51449 #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 2-CHLORO-6-FLUORO-N-[4-[3-(TRIFLUOROM | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.03 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / 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: 2.1→46.54 Å / Num. obs: 42558 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 43.49 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L0L Resolution: 2.1→46.54 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9352 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.149
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Displacement parameters | Biso mean: 50.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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