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Yorodumi- PDB-2z6w: Crystal structure of human cyclophilin D in complex with cyclosporin A -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6w | ||||||
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Title | Crystal structure of human cyclophilin D in complex with cyclosporin A | ||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN D | ||||||
Function / homology | Function and homology information 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 / 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 | HOMO SAPIENS (human) TOLYPOCLADIUM INFLATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å | ||||||
Authors | Kajitani, K. / Fujihashi, M. / Kobayashi, Y. / Shimizu, S. / Tsujimoto, Y. / Miki, K. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal Structure of Human Cyclophilin D in Complex with its Inhibitor, Cyclosporin a at 0.96-A Resolution. Authors: Kajitani, K. / Fujihashi, M. / Kobayashi, Y. / Shimizu, S. / Tsujimoto, Y. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6w.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6w.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6w ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6w | HTTPS FTP |
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-Related structure data
Related structure data | 2bitS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17783.322 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-165 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: PPIF, CYP3 / Plasmid: PET-21A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30405, peptidylprolyl isomerase #2: Protein/peptide | Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | Compound details | CYCLOSPORI | Sequence details | THE N-TERMINAL MET CHAINS A AND B IS AN ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | pH: 2.9 Details: 20% PEG 3350, PH 2.9, VAPOR DIFFUSION, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: BL41XU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 0.96→200 Å / Num. obs: 180558 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 0.96→0.97 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.4 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BIT Resolution: 0.96→56.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.498 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 8.23 Å2
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Refinement step | Cycle: LAST / Resolution: 0.96→56.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.96→0.98 Å / Total num. of bins used: 20
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