+Open data
-Basic information
Entry | Database: PDB / ID: 5noy | ||||||
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Title | Structure of cyclophilin A in complex with 3,4-diaminobenzamide | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 | 5noy.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5noy.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 5noy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5noy_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 5noy_full_validation.pdf.gz | 417.8 KB | Display | |
Data in XML | 5noy_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5noy_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5noy ftp://data.pdbj.org/pub/pdb/validation_reports/no/5noy | HTTPS FTP |
-Related structure data
Related structure data | 5noqC 5norC 5nosC 5notC 5nouC 5novC 5nowC 5noxC 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-93K / |
#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: 2.83 Å3/Da / Density % sol: 56.49 % |
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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: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→38.49 Å / Num. obs: 38376 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2643 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LUD Resolution: 1.43→38.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.944 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.055 / 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: 18.09 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→38.49 Å
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