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- PDB-8fb1: HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fb1 | ||||||
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Title | HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 6a ANDINDAZOLE ACID BOUND IN H12-POCKET | ||||||
![]() | Nuclear receptor ROR-gamma | ||||||
![]() | DNA BINDING PROTEIN / RORC2 / RORgammat / structure-based design / macrocyclization / topical delivery | ||||||
Function / homology | ![]() T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / 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 ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vajdos, F.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists. Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, ...Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, A.L. / Knafels, J.D. / Vazquez, M.L. / Berstein, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | 89.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8favC ![]() 8fb2C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30250.811 Da / Num. of mol.: 2 / Mutation: C278S, C345S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 100 mM MES pH 5.9, 5 mM ammonium sulfate, 300 mM magnesium chloride, 10% N,N-dimethylformamide, and 14% PEG-MME-5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→96.49 Å / Num. obs: 26306 / % possible obs: 98.5 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Net I/σ(I): 11.1 / Num. measured all: 86048 |
Reflection shell | Resolution: 2.18→2.67 Å / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.404 / Num. measured all: 38851 / Num. unique obs: 11965 / CC1/2: 0.85 / Rpim(I) all: 0.262 / Rrim(I) all: 0.483 / Net I/σ(I) obs: 3.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RORG5_IA_DIMER_P21.PDB Resolution: 2.18→56.78 Å / SU B: 14.387 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.233 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES RESIDUAL ONLY
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Displacement parameters | Biso mean: 24.435 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→56.78 Å
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