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Yorodumi- PDB-1fkl: ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fkl | ||||||
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Title | ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX | ||||||
Components | FK506 BINDING PROTEIN | ||||||
Keywords | ROTAMASE / FK506 BINDING PROTEIN / FKBP12 / FKBP / CIS-TRANS PROLYL-ISOMERASE | ||||||
Function / homology | Function and homology information mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / : / cytoplasmic side of membrane / activin binding / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / ryanodine receptor complex ...mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / : / cytoplasmic side of membrane / activin binding / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / ryanodine receptor complex / regulation of amyloid precursor protein catabolic process / response to caffeine / ventricular cardiac muscle tissue morphogenesis / FK506 binding / negative regulation of ryanodine-sensitive calcium-release channel activity / SMAD binding / protein peptidyl-prolyl isomerization / regulation of immune response / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / heart morphogenesis / T cell proliferation / muscle contraction / supramolecular fiber organization / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytokine-mediated signaling pathway / Z disc / positive regulation of protein binding / regulation of protein localization / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / protein homodimerization activity / extracellular exosome / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Wilson, K.P. / Sintchak, M.D. / Thomson, J.A. / Navia, M.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin. Authors: Wilson, K.P. / Yamashita, M.M. / Sintchak, M.D. / Rotstein, S.H. / Murcko, M.A. / Boger, J. / Thomson, J.A. / Fitzgibbon, M.J. / Black, J.R. / Navia, M.A. #1: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: X-Ray Structure of Calcineurin Inhibited by the Immunophilin-Immunosuppressant Fkbp12-Fk506 Complex Authors: Griffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes Authors: Rotonda, J. / Burbaum, J.J. / Chan, H.K. / Marcy, A.I. / Becker, J.W. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818 Authors: Becker, J.W. / Rotonda, J. / Mckeever, B.M. / Chan, H.K. / Marcy, A.I. / Wiederrecht, G. / Hermes, J.D. / Springer, J.P. #4: Journal: J.Mol.Biol. / Year: 1993 Title: Atomic Structures of Human Immunophilin Fkbp12 Complexes with Fk506 and Rapamycin Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J. #5: Journal: J.Am.Chem.Soc. / Year: 1991 Title: Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex Authors: Van Duyne, G.D. / Standaert, R.F. / Schreiber, S.L. / Clardy, J. #6: Journal: Science / Year: 1991 Title: Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fkl.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fkl.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fkl_validation.pdf.gz | 475 KB | Display | wwPDB validaton report |
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Full document | 1fkl_full_validation.pdf.gz | 477.4 KB | Display | |
Data in XML | 1fkl_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1fkl_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/1fkl ftp://data.pdbj.org/pub/pdb/validation_reports/fk/1fkl | HTTPS FTP |
-Related 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: 11794.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MR 12,000 DALTONS / Source: (natural) Bos taurus (cattle) / Organ: THYMUS / References: UniProt: P18203, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-RAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 1.7→7 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_improper_angle_deg / Dev ideal: 1.24 |