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- PDB-4zsd: Human Cyclophilin D Complexed with an Inhibitor at room temperature -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zsd | ||||||
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Title | Human Cyclophilin D Complexed with an Inhibitor at room temperature | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
![]() | ISOMERASE / isomerase inhibitor complex | ||||||
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 / necroptotic process / apoptotic mitochondrial changes / 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 / peptide binding / 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 | ![]() ![]() | ||||||
![]() | Gelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.-L. / Labesse, G. / Guichou, J.-F. | ||||||
![]() | ![]() Title: Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography. Authors: Gelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.L. / Labesse, G. / Guichou, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 60 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3rdcC ![]() 4xldC ![]() 4xn6C ![]() 4xncC ![]() 4xneC ![]() 4xoyC ![]() 4xozC ![]() 4xp0C ![]() 4xp2C ![]() 4xp3C ![]() 4xrjC ![]() 4xrlC ![]() 4zscC 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
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: UNP residues 44-207 / Mutation: K133I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-7I6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→57.94 Å / Num. obs: 25914 / % possible obs: 99.2 % / Redundancy: 2 % / Net I/σ(I): 7 |
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Processing
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Refinement | Resolution: 1.45→48.49 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.052 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.15 Å2 / Biso mean: 12.549 Å2 / Biso min: 5.86 Å2
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Refinement step | Cycle: final / Resolution: 1.45→48.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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