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Yorodumi- PDB-4xnc: Crystal structure at room temperature of cyclophilin D in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xnc | ||||||
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Title | Crystal structure at room temperature of cyclophilin D in complex with an inhibitor | ||||||
Components | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
Keywords | ISOMERASE / inhibitor isomerase fragment based drug design | ||||||
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 / apoptotic mitochondrial changes / necroptotic process / negative regulation of intrinsic apoptotic signaling pathway / protein peptidyl-prolyl isomerization / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Gelin, M. / Allemand, F. / Labesse, G. / Guichou, J.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xnc.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xnc.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/4xnc ftp://data.pdbj.org/pub/pdb/validation_reports/xn/4xnc | HTTPS FTP |
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-Related structure data
Related structure data | 3rdcC 4xldC 4xn6C 4xneC 4xoyC 4xozC 4xp0C 4xp2C 4xp3C 4xrjC 4xrlC 4zscC 4zsdC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: Residues 44-207 / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-EA4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 25% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→29.5 Å / Num. obs: 6820 / % possible obs: 98.1 % / Redundancy: 4.5 % / Net I/σ(I): 18.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→29.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.578 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.192 / 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: 40.42 Å2 / Biso mean: 17.087 Å2 / Biso min: 6.72 Å2
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Refinement step | Cycle: final / Resolution: 2.23→29.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.233→2.291 Å / Total num. of bins used: 20
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