+Open data
-Basic information
Entry | Database: PDB / ID: 1c9h | ||||||
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Title | CRYSTAL STRUCTURE OF FKBP12.6 IN COMPLEX WITH RAPAMYCIN | ||||||
Components | FKBP12.6FKBP1B | ||||||
Keywords | IMMUNE SYSTEM / FKBP12 / RAPAMYCIN / COMPLEX / RYANODINE RECEPTOR | ||||||
Function / homology | Function and homology information positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / : / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Deivanayagam, C.C.S. / Carson, M. / Thotakura, A. / Narayana, S.V.L. / Chodavarapu, C.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of FKBP12.6 in complex with rapamycin. Authors: Deivanayagam, C.C. / Carson, M. / Thotakura, A. / Narayana, S.V. / Chodavarapu, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c9h.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9h.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 1c9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9h ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9h | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 11667.305 Da / Num. of mol.: 1 / Fragment: FKBP12.6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / Organ: BRAIN / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / References: UniProt: P68106 |
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#2: Chemical | ChemComp-RAP / |
#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: 2.49 Å3/Da / Density % sol: 50.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 4000, LITHIUM SULFATE, HEPES BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 105747 / Num. obs: 7941 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.247 / % possible all: 86.6 |
Reflection shell | *PLUS % possible obs: 86.6 % |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 783518.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.39 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'CNS 0.4, O, OOPS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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