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Yorodumi- PDB-8chq: The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-3,5-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8chq | ||||||
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Title | The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsulfonimidoyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / FKBP51 / Inhibitor | ||||||
Function / homology | Function and homology information FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å | ||||||
Authors | Meyners, C. / Purder, P.L. / Hausch, F. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Jacs Au / Year: 2023 Title: Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues. Authors: Purder, P.L. / Meyners, C. / Sugiarto, W.O. / Kolos, J. / Lohr, F. / Gebel, J. / Nehls, T. / Dotsch, V. / Lermyte, F. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8chq.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8chq.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 8chq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8chq ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8chq | HTTPS FTP |
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-Related structure data
Related structure data | 8chiC 8chjC 8chkC 8chlC 8chmC 8chnC 8chpC 8chrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14004.026 Da / Num. of mol.: 1 / Mutation: A19T, C103A, C107I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-UMR / ( |
#3: 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: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG3350, 0.2 M ammonium acetate, 0.1M HEPES-NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2022 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.01→42.35 Å / Num. obs: 68384 / % possible obs: 98.4 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.017 / Rrim(I) all: 0.034 / Net I/σ(I): 25.4 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→39.363 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.591 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.947 Å2
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Refinement step | Cycle: LAST / Resolution: 1.01→39.363 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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