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Yorodumi- PDB-4drn: EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4drn | ||||||
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Title | EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51 WITH {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1S,2R)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophilin / peptidyl-prolyl isomerase | ||||||
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: 1.069 Å | ||||||
Authors | Gopalakrishnan, R. / Kozany, C. / Gaali, S. / Kress, C. / Hoogeland, B. / Bracher, A. / Hausch, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Evaluation of Synthetic FK506 Analogues as Ligands for the FK506-Binding Proteins 51 and 52. Authors: Gopalakrishnan, R. / Kozany, C. / Gaali, S. / Kress, C. / Hoogeland, B. / Bracher, A. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4drn.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4drn.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 4drn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4drn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4drn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4drn_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4drn_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/4drn ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4drn | HTTPS FTP |
-Related structure data
Related structure data | 4drkC 4drmC 4droC 4drpC 3o5qS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | biological unit is a monomer |
-Components
#1: Protein | Mass: 14026.077 Da / Num. of mol.: 1 / Fragment: UNP residues 16-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-0MC / { |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 37.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES pH 7.5, 10 % DMSO, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.069→25.057 Å / Num. all: 62752 / Num. obs: 62752 / % possible obs: 95.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.05 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O5Q Resolution: 1.069→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1649 / WRfactor Rwork: 0.1517 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9093 / SU B: 0.849 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0291 / SU Rfree: 0.0289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.86 Å2 / Biso mean: 13.5351 Å2 / Biso min: 6.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.069→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.069→1.097 Å / Total num. of bins used: 20
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