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Open data
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Basic information
Entry | Database: PDB / ID: 3rdc | ||||||
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Title | Human Cyclophilin D Complexed with an Inhibitor | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
![]() | ISOMERASE/ISOMERASE INHIBITOR / beta barrel / prolyl cis/trans isomerase / mitochondria / inhibitor / 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 / 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 | ![]() ![]() | ||||||
![]() | Colliandre, L. / Ahmed-Belkacem, H. / Bessin, Y. / Pawlotsky, J.M. / 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. #1: ![]() Title: Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities. Authors: Ahmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. / Krimm, I. / Pawlotsky, J.M. / 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 | ![]() | 50.4 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 644.9 KB | Display | ![]() |
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Full document | ![]() | 644.8 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xldC ![]() 4xn6C ![]() 4xncC ![]() 4xneC ![]() 4xoyC ![]() 4xozC ![]() 4xp0C ![]() 4xp2C ![]() 4xp3C ![]() 4xrjC ![]() 4xrlC ![]() 4zscC ![]() 4zsdC ![]() 2bitS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17870.400 Da / Num. of mol.: 1 / Fragment: UNP residues 43-207 / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EA4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 12, 2008 |
Radiation | Monochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→28.2 Å / Num. all: 10623 / Num. obs: 10358 / % possible obs: 97.5 % / Observed criterion σ(I): 9.1 / Redundancy: 4.1 % / Rsym value: 0.059 |
Reflection shell | Resolution: 1.93→1.987 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.188 / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BIT Resolution: 1.94→25.79 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.853 / SU B: 4.259 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.201 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.287 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→25.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.937→1.987 Å / Total num. of bins used: 20
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