+Open data
-Basic information
Entry | Database: PDB / ID: 5ccs | ||||||
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Title | Human Cyclophilin D Complexed with Inhibitor | ||||||
Components | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
Keywords | ISOMERASE / Cyclophilin / complex / inhibitor | ||||||
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 / peptide binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. ...Gibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. / Sutton, R. / Lian, L.Y. | ||||||
Citation | Journal: To Be Published Title: Human Cyclophilin D Complexed with Inhibitor Authors: Gibson, R.P. / Shore, E. / Kershaw, N. / Awais, M. / Javed, A. / Latawiec, D. / Pandalaneni, S. / Wen, L. / Berry, N. / O'Neill, P. / Sutton, R. / Lian, L.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ccs.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ccs.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ccs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5ccs ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5ccs | HTTPS FTP |
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-Related structure data
Related structure data | 5cbtC 5cbvC 5ccnC 5ccqC 5ccrC 6y3eC 2bitS S: Starting model for refinement 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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-Components
#1: Protein | Mass: 17782.271 Da / Num. of mol.: 1 / Fragment: UNP residues 44-207 / Mutation: K125Q K133I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30405, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-C4Y / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% w/v PEG3350, 0.1M TRIS-HCL pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9794 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.7 Å / Num. obs: 8627 / % possible obs: 63.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 7 / % possible all: 67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BIT Resolution: 2.1→46.69 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.297 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.193 / 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: 14.48 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→46.69 Å
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Refine LS restraints |
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