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Yorodumi- PDB-8baj: Structure of the FK1 domain of the FKBP51 G64S variant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8baj | ||||||
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Title | Structure of the FK1 domain of the FKBP51 G64S variant in complex with (1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / Isomerase Inhibitor Complex | ||||||
Function / homology | Function and homology information FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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: 1.2 Å | ||||||
Authors | Meyners, C. / Hausch, F. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Binding pocket stabilization by high-throughput screening of yeast display libraries. Authors: Lerma Romero, J.A. / Meyners, C. / Christmann, A. / Reinbold, L.M. / Charalampidou, A. / Hausch, F. / Kolmar, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8baj.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8baj.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 8baj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/8baj ftp://data.pdbj.org/pub/pdb/validation_reports/ba/8baj | HTTPS FTP |
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-Related structure data
Related structure data | 7r0lC 8ba6C 5obkS S: Starting model for refinement 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: 14034.053 Da / Num. of mol.: 1 / Mutation: A19T C103A C107I G64S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-9QN / ( |
#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: 2.24 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 40% PEG3350 0.1M HEPES-NaOH pH 7.5 0.2M ammonium acetate |
-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: Mar 18, 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: 1.2→40.86 Å / Num. obs: 39512 / % possible obs: 98.4 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.068 / Rrim(I) all: 0.134 / Net I/σ(I): 5.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OBK Resolution: 1.2→39.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.064 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045 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: 13.269 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→39.28 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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