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Yorodumi- PDB-6x4q: Human cyclophilin A bound to a series of acylcic and macrocyclic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x4q | ||||||
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Title | Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-14-cyclobutyl-2,11,17,17-tetramethyl-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 33) | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / Cyclophilin A / Sanglifehrin A / prolyl isomerase / macrocylcic inhibitor / peptidomimetic / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Appleby, T.C. / Paulsen, J.L. / Schmitz, U. / Shivakumar, D. | ||||||
Citation | Journal: J.Chem.Inf.Model. / Year: 2020 Title: Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. Authors: Paulsen, J.L. / Yu, H.S. / Sindhikara, D. / Wang, L. / Appleby, T. / Villasenor, A.G. / Schmitz, U. / Shivakumar, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x4q.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x4q.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 6x4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x4q_validation.pdf.gz | 831.1 KB | Display | wwPDB validaton report |
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Full document | 6x4q_full_validation.pdf.gz | 831.2 KB | Display | |
Data in XML | 6x4q_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6x4q_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x4q ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x4q | HTTPS FTP |
-Related structure data
Related structure data | 6x3rC 6x3yC 6x4mC 6x4nC 6x4oC 6x4pC 2cplS 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: 18231.701 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-UOJ / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG 3350, 5% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.04 Å / Num. obs: 19493 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.34 Å2 / Rsym value: 0.051 / Net I/σ(I): 27.79 |
Reflection shell | Resolution: 1.8→1.85 Å / Num. unique obs: 1349 / Rsym value: 0.412 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CPL Resolution: 1.8→34.04 Å / SU ML: 0.1404 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6575 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.04 Å
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Refine LS restraints |
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LS refinement shell |
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