+Open data
-Basic information
Entry | Database: PDB / ID: 5lud | |||||||||
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Title | Structure of Cyclophilin A in complex with 2,3-Diaminopyridine | |||||||||
Components | Peptidyl-prolyl cis-trans isomeraseProlyl isomerase | |||||||||
Keywords | ISOMERASE / LIGAND COMPLEX / BETA BARREL / PROLYL CIS/TRANS ISOMERASE | |||||||||
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 / negative regulation of stress-activated MAPK cascade / 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 / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / virion binding / 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 / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet aggregation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / protein folding / integrin binding / Platelet degranulation / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å | |||||||||
Authors | McNae, I.W. / Nowicki, M.W. / Blackburn, E.A. / Wear, M.A. / Walkinshaw, M.D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: FEBS Open Bio / Year: 2017 Title: Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using BiacoreTM T200. Authors: Wear, M.A. / Nowicki, M.W. / Blackburn, E.A. / McNae, I.W. / Walkinshaw, M.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lud.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lud.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5lud ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lud | HTTPS FTP |
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-Related structure data
Related structure data | 4n1mS S: Starting model for refinement |
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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: HEL-S-69p / Production host: Escherichia coli (E. coli) References: UniProt: V9HWF5, UniProt: P62937*PLUS, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-76X / |
#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: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris, PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→46.15 Å / Num. obs: 55267 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1 / CC1/2: 0.443 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4n1m Resolution: 1.25→46.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.994 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.751 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→46.14 Å
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