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- PDB-6ra1: Human Cyclophilin D in complex with norbornane fragment derivative -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ra1 | ||||||
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Title | Human Cyclophilin D in complex with norbornane fragment derivative | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
![]() | ISOMERASE / CYCLOPHILIN / BETA BARREL / PROLYL CIS/TRANS ISOMERASE / MITOC | ||||||
Function / homology | ![]() regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / necroptotic process / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Graedler, U. | ||||||
![]() | ![]() Title: Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies. Authors: Gradler, U. / Schwarz, D. / Blaesse, M. / Leuthner, B. / Johnson, T.L. / Bernard, F. / Jiang, X. / Marx, A. / Gilardone, M. / Lemoine, H. / Roche, D. / Jorand-Lebrun, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.7 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8lC ![]() 6r8oC ![]() 6r8wC ![]() 6r9sC ![]() 6r9uC ![]() 6r9xC ![]() 4j5bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 85 molecules ![](data/chem/img/JWB.gif)
![](data/chem/img/JVQ.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JVQ.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JWB / | ||
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#3: Chemical | ChemComp-JVQ / | ||
#4: Chemical | ChemComp-PEG / | ||
#5: Chemical | ChemComp-PG4 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 50 mM potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.09 Å / Num. obs: 12987 / % possible obs: 95.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.48 Å2 / Rsym value: 0.113 / Net I/σ(I): 11.01 |
Reflection shell | Resolution: 2→2.25 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.04 / Num. unique obs: 3834 / Rsym value: 0.514 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J5B Resolution: 2→40.23 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.15
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Displacement parameters | Biso mean: 25.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -10.371 Å / Origin y: -8.76 Å / Origin z: -23.1023 Å
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Refinement TLS group | Selection details: { A|* } |