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- PDB-6r9x: Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-yl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r9x | ||||||
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Title | Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-ylmethyl-oxalamide | ||||||
![]() | 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 | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
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Full document | ![]() | 426.4 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8lC ![]() 6r8oC ![]() 6r8wC ![]() 6r9sC ![]() 6r9uC ![]() 6ra1C ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: 44-207 (K175I) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-JW2 / ~{ |
#3: Water | ChemComp-HOH / |
Sequence details | ALIGNMENT: - Global alignment of extracted AA sequence from the pdb file with the original sequence ...ALIGNMENT: - Global alignment of extracted AA sequence from the pdb file with the original sequence inserted in the template - Be aware that the alignment is the best one for the given scoring schemata but does not have to be the best one out of all kinds of possible alignments! - No substitution matrix used. Just matches, mismatches and gaps ar considered - The first sequence was extracted from the xml-template file according to the chosen template. The second sequence was extract from the ATOM section of the pdb file. GNPLVYLDVD |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→87.6 Å / Num. obs: 16838 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.14 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.51 |
Reflection shell | Resolution: 1.66→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.195 / Num. unique obs: 5436 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J5B Resolution: 1.66→15.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.1
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Displacement parameters | Biso mean: 10.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→15.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.68 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 12.2253 Å / Origin y: 14.0753 Å / Origin z: 23.6711 Å
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Refinement TLS group | Selection details: { A|* } |