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Yorodumi- PDB-5nos: Structure of cyclophilin A in complex with 3-amino-1H-pyridin-2-one -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nos | ||||||
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Title | Structure of cyclophilin A in complex with 3-amino-1H-pyridin-2-one | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | ISOMERASE / LIGAND COMPLEX / BETA BARREL / PROLYL CIS/TRANS ISOMERASE / CYTOSOLIC | ||||||
Function / homology | Function and homology information negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / 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 / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / 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 / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / 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 / molecular replacement / Resolution: 1.35 Å | ||||||
Authors | Georgiou, C. / Mcnae, I.W. / Ioannidis, H. / Julien, M. / Walkinshaw, M.D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders. Authors: Georgiou, C. / McNae, I. / Wear, M. / Ioannidis, H. / Michel, J. / Walkinshaw, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nos.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nos.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nos_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 5nos_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 5nos_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 5nos_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5nos ftp://data.pdbj.org/pub/pdb/validation_reports/no/5nos | HTTPS FTP |
-Related structure data
Related structure data | 5noqC 5norC 5notC 5nouC 5novC 5nowC 5noxC 5noyC 5nozC 5ludS 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-92Z / |
#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: 2.73 Å3/Da / Density % sol: 54.98 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→45.25 Å / Num. obs: 43795 / % possible obs: 99.2 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2053 / % possible all: 96 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LUD Resolution: 1.35→45.24 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.189 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / 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: 15.096 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→45.24 Å
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