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Open data
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Basic information
Entry | Database: PDB / ID: 5cbv | ||||||
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Title | Human Cyclophilin D Complexed with Inhibitor | ||||||
![]() | Human Cyclophilin D | ||||||
![]() | ISOMERASE / cyclophilin / complex / inhibitor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 34.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 657.4 KB | Display | ![]() |
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Full document | ![]() | 658.3 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cbtC ![]() 5ccnC ![]() 5ccqC ![]() 5ccrC ![]() 5ccsC ![]() 6y3eC ![]() 2bitS S: Starting model for refinement 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17783.322 Da / Num. of mol.: 1 / Fragment: residues 44-207 / Mutation: K133I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 139 molecules ![](data/chem/img/K.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/4ZP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/4ZP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-K / |
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#3: Chemical | ChemComp-FMT / |
#4: Chemical | ChemComp-PG4 / |
#5: Chemical | ChemComp-PGE / |
#6: Chemical | ChemComp-4ZP / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 4M potassium formate, 0.1M BIS-TRIS propane pH 9, 2% w/v PEG 2000mme |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38.2 Å / Num. obs: 17797 / % possible obs: 98.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 11 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2bit Resolution: 1.8→38.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.831 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / 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: 13.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.2 Å
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