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Yorodumi- PDB-1zkf: Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zkf | ||||||
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Title | Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA | ||||||
Components |
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Keywords | ISOMERASE/ISOMERASE SUBSTRATE / CypA / Cyclophilin-A / Cyclophilin / PPIASE / PROLYL-ISOMERASE / ISOMERASE / ISOMERASE-ISOMERASE SUBSTRATE 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 / 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 / Binding and entry of HIV virion / positive regulation of viral genome replication / 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Eisenmesser, E.Z. / Thai, V. / Pozharski, E. / Kern, D. | ||||||
Citation | Journal: To be Published Title: Mechanistic Insights of Cyclophilin-A from X-Ray Cyrstallographic and Nuclear Magnet Resonance Investigations Authors: Eisenmesser, E.Z. / Thai, V. / Pozharski, E. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zkf.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zkf.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zkf_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 1zkf_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 1zkf_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1zkf_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zkf ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zkf | HTTPS FTP |
-Related structure data
Related structure data | 1rmhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18036.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62937, peptidylprolyl isomerase #2: Protein/peptide | Mass: 610.615 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE PEPTIDE SUBSTRATE WAS PURCHASED FROM Bachem (King of Prussia, PA). #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 32.2457 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.2 Details: Ammonium Sulfate, Tris-HCL, Sodium Azide, Dimethyl Sulfoxide, Glycerol, pH 8.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2003 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→38 Å / Num. all: 15878 / Num. obs: 15797 / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Rmerge(I) obs: 0.144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RMH Resolution: 2.55→38 Å / σ(F): 10.2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→38 Å
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Xplor file |
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