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- PDB-3odi: Crystal structure of cyclophilin A in complex with Voclosporin E-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3odi | ||||||
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Title | Crystal structure of cyclophilin A in complex with Voclosporin E-ISA247 | ||||||
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![]() | ISOMERASE/IMMUNOSUPPRESSANT / CALCINEURIN INHIBITION / CALCINEURIN / CYCLOSPORIN / PSORIASIS / IMMUNOSUPPRESSANT / VOCLOSPORIN / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX | ||||||
Function / homology | ![]() negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / response to hypoxia / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Stihle, M. / Benz, J. / Hennig, M. | ||||||
![]() | ![]() Title: Structural basis for the cyclophilin A binding affinity and immunosuppressive potency of E-ISA247 (voclosporin). Authors: Kuglstatter, A. / Mueller, F. / Kusznir, E. / Gsell, B. / Stihle, M. / Thoma, R. / Benz, J. / Aspeslet, L. / Freitag, D. / Hennig, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 371.5 KB | Display | ![]() |
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PDB format | ![]() | 305.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 583 KB | Display | ![]() |
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Full document | ![]() | 614.8 KB | Display | |
Data in XML | ![]() | 84.7 KB | Display | |
Data in CIF | ![]() | 114.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3odlC ![]() 2rmaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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10 | ![]()
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Unit cell |
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Details | The asymmetric unit of the crystal contains ten pharmacological units. |
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Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A8K220, UniProt: P62937*PLUS, peptidylprolyl isomerase #2: Protein/peptide | Mass: 1232.635 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: A MODIFIED CYCLOSPORIN A / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Compound details | VOCLOSPORIN IS A CYCLOSPORIN ANALOG, A CYCLIC UNDECAPEPTIDE. HERE, VOCLOSPORIN IS REPRESENTED BY ...VOCLOSPORI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG3350, 0.1M MES, 0.2M ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 93907 / % possible obs: 91.8 % / Redundancy: 3.3 % / Rsym value: 0.082 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.399 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2RMA Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.43 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.425 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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