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- PDB-6r8l: Human Cyclophilin D in complex with 1-((1S,9S,10S)-10-Hydroxy-12-... -
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Basic information
Entry | Database: PDB / ID: 6r8l | ||||||
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Title | Human Cyclophilin D in complex with 1-((1S,9S,10S)-10-Hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2,4,6-trien-4-ylmethyl)-3- {2-[(R)-2-(2-methylsulfanyl-phenyl)-pyrrolidin-1-yl]-2-oxo-ethyl}-urea | ||||||
![]() | 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 | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 681.6 KB | Display | ![]() |
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Full document | ![]() | 681.5 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8oC ![]() 6r8wC ![]() 6r9sC ![]() 6r9uC ![]() 6r9xC ![]() 6ra1C ![]() 4j5bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: 44-207 (K175I) / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-JUZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82655 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→51.21 Å / Num. obs: 23444 / % possible obs: 96.8 % / Redundancy: 2.73 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.79 |
Reflection shell | Resolution: 1.64→1.89 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 7936 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J5B Resolution: 1.64→51.21 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9313 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.085
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Displacement parameters | Biso mean: 28.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.234 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→51.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.71 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -10.397 Å / Origin y: -8.544 Å / Origin z: -23.029 Å
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Refinement TLS group | Selection details: { A|44 - A|207 } |