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Open data
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Basic information
Entry | Database: PDB / ID: 6gjm | ||||||
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Title | Cyclophilin A complexed with tri-vector ligand 4. | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase A | ||||||
![]() | ISOMERASE / Cyclophilins / CypA / inhibitor / PPIase / 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 | ![]() ![]() ![]() | ||||||
![]() | Georgiou, C. / De Simone, A. / Walkinshaw, M.D. / Michel, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. Authors: De Simone, A. / Georgiou, C. / Ioannidis, H. / Gupta, A.A. / Juarez-Jimenez, J. / Doughty-Shenton, D. / Blackburn, E.A. / Wear, M.A. / Richards, J.P. / Barlow, P.N. / Carragher, N. / ...Authors: De Simone, A. / Georgiou, C. / Ioannidis, H. / Gupta, A.A. / Juarez-Jimenez, J. / Doughty-Shenton, D. / Blackburn, E.A. / Wear, M.A. / Richards, J.P. / Barlow, P.N. / Carragher, N. / Walkinshaw, M.D. / Hulme, A.N. / Michel, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.3 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.2 KB | Display | ![]() |
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Full document | ![]() | 418.2 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gjiC ![]() 6gjjC ![]() 6gjlC ![]() 6gjnC ![]() 6gjpC ![]() 6gjrC ![]() 6gjyC ![]() 5noyS 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
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-L36 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.24 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.354→87.283 Å / Num. obs: 45033 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.354→1.377 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2216 / CC1/2: 0.91 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NOY Resolution: 1.354→34.04 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.415 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.01 / ESU R Free: 0.01 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.723 Å2
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Refinement step | Cycle: 1 / Resolution: 1.354→34.04 Å
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Refine LS restraints |
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