+Open data
-Basic information
Entry | Database: PDB / ID: 6gjy | ||||||
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Title | Cyclophilin A complexed with tri-vector ligand 5. | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | ISOMERASE / Cyclophilins / CypA / inhibitor / PPIase / complex | ||||||
Function / homology | Function and homology information 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 / virion binding / leukocyte chemotaxis / endothelial cell activation ...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 / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / 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 / viral release from host cell / Calcineurin activates NFAT / protein peptidyl-prolyl isomerization / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / platelet aggregation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / Platelet degranulation / protein folding / 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 / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Georgiou, C. / De Simone, A. / Walkinshaw, M.D. / Michel, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gjy.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gjy.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gjy_validation.pdf.gz | 897.4 KB | Display | wwPDB validaton report |
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Full document | 6gjy_full_validation.pdf.gz | 898.1 KB | Display | |
Data in XML | 6gjy_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6gjy_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/6gjy ftp://data.pdbj.org/pub/pdb/validation_reports/gj/6gjy | HTTPS FTP |
-Related structure data
Related structure data | 6gjiC 6gjjC 6gjlC 6gjmC 6gjnC 6gjpC 6gjrC 5noyS 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: 18036.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-F1Z / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.90001 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90001 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→45.3 Å / Num. obs: 50202 / % possible obs: 98.89 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.29→1.31 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 12564 / CC1/2: 0.505 / Rpim(I) all: 0.602 / % possible all: 98.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NOY Resolution: 1.29→45.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.162 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.046 / 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: 21.798 Å2
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Refinement step | Cycle: 1 / Resolution: 1.29→45.3 Å
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Refine LS restraints |
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