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- PDB-6vct: Mucor circinelloides FKBP12 protein bound with APX879 in C2221 sp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vct | |||||||||
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Title | Mucor circinelloides FKBP12 protein bound with APX879 in C2221 space group | |||||||||
![]() | Peptidylprolyl isomerase | |||||||||
![]() | ISOMERASE / FK506-binding protein 1A / FKBP12 / FK506 | |||||||||
Function / homology | FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Chem-R27 / peptidylprolyl isomerase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gobeil, S. / Spicer, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs. Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D. #1: ![]() Title: Designing Selective and Non-Immunosuppressive Antifungal FK506 Analogs: Structures, Biophysics and Dynamics of Fungal and Human Calcineurin-Inhibitor Complexes Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 26 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370 KB | Display | ![]() |
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Full document | ![]() | 372.6 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vcuC ![]() 6vcvC ![]() 6vrxC ![]() 5huaS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12095.665 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-R27 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1600mM Sodium Citrate Tribasic |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 7938 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 17.55 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Rsym value: 0.078 / Net I/av σ(I): 56.9 / Net I/σ(I): 56.9 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 19.1 / Num. unique obs: 385 / CC1/2: 0.994 / Rpim(I) all: 0.045 / Rrim(I) all: 0.176 / Rsym value: 0.17 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HUA Resolution: 1.94→32.81 Å / SU ML: 0.1546 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0015 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→32.81 Å
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Refine LS restraints |
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LS refinement shell |
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