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Yorodumi- PDB-7npc: ROR(gamma)t ligand binding domain in complex with allosteric liga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7npc | ||||||||||||||||||
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Title | ROR(gamma)t ligand binding domain in complex with allosteric ligand FM156 | ||||||||||||||||||
Components | Nuclear receptor ROR-gamma | ||||||||||||||||||
Keywords | NUCLEAR PROTEIN / Nuclear Receptor / Allosteric / Inverse Agonist / Inhibitor | ||||||||||||||||||
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 / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian regulation of gene expression / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / 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: 1.47 Å | ||||||||||||||||||
Authors | de Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L. | ||||||||||||||||||
Funding support | Netherlands, 5items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Activity Relationship Studies of Trisubstituted Isoxazoles as Selective Allosteric Ligands for the Retinoic-Acid-Receptor-Related Orphan Receptor gamma t. Authors: Meijer, F.A. / Saris, A.O.W.M. / Doveston, R.G. / Oerlemans, G.J.M. / de Vries, R.M.J.M. / Somsen, B.A. / Unger, A. / Klebl, B. / Ottmann, C. / Cossar, P.J. / Brunsveld, L. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7npc.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7npc.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 7npc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7npc_validation.pdf.gz | 757.2 KB | Display | wwPDB validaton report |
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Full document | 7npc_full_validation.pdf.gz | 757.5 KB | Display | |
Data in XML | 7npc_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7npc_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7npc ftp://data.pdbj.org/pub/pdb/validation_reports/np/7npc | HTTPS FTP |
-Related structure data
Related structure data | 7necC 7np5C 7np6C 6salS S: Starting model for refinement C: citing same article (ref.) |
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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: 28071.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449 |
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#2: Chemical | ChemComp-ULT / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: 1.6 M AmSO4, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→68.24 Å / Num. obs: 58535 / % possible obs: 100 % / Redundancy: 113.1 % / CC1/2: 1 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.47→1.5 Å / Num. unique obs: 2855 / CC1/2: 0.382 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6sal Resolution: 1.47→53.86 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.164 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.724 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→53.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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