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Yorodumi- PDB-7b9y: Structure of the FKBP51FK1 domain in complex with the macrocyclic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b9y | ||||||
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Title | Structure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 64a | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / Inhibitor / Complex / SAFit / FKBP | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bauder, M. / Meyners, C. / Purder, P. / Merz, S. / Voll, A. / Heymann, T. / Hausch, F. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors. Authors: Bauder, M. / Meyners, C. / Purder, P.L. / Merz, S. / Sugiarto, W.O. / Voll, A.M. / Heymann, T. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b9y.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b9y.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 7b9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b9y_validation.pdf.gz | 766 KB | Display | wwPDB validaton report |
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Full document | 7b9y_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 7b9y_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7b9y_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/7b9y ftp://data.pdbj.org/pub/pdb/validation_reports/b9/7b9y | HTTPS FTP |
-Related structure data
Related structure data | 7a6wC 7a6xC 7awxC 7b9zC 7ba0C 4tw7S 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: 14273.369 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-T5B / |
#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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% PEG 3350, 0.1 M HEPES 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.35→105.93 Å / Num. obs: 32570 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Net I/σ(I): 21.1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4tw7 Resolution: 1.35→39.003 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.139 / SU B: 1.45 / SU ML: 0.027 / Average fsc free: 0.9671 / Average fsc work: 0.9723 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.044 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: 22.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→39.003 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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