+Open data
-Basic information
Entry | Database: PDB / ID: 2alf | ||||||
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Title | crystal structure of human CypA mutant K131A | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | 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 / virion binding / 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 / 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 aggregation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hu, H. / Huang, C.-Q. / Liu, H.-L. / Han, Y. / Chen, M.-E. / Yu, L. / Bi, R.-C. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Nuclease activity of Cyclophilin A and its structural basis Authors: Hu, H. / Huang, C.-Q. / Liu, H.-L. / Han, Y. / Chen, M.-E. / Yu, L. / Bi, R.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2alf.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2alf.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 2alf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/2alf ftp://data.pdbj.org/pub/pdb/validation_reports/al/2alf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17847.271 Da / Num. of mol.: 1 / Mutation: K131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CyPA / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62937, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-MG / |
#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: 2.196073 Å3/Da / Density % sol: 43.55156 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 8.5 Details: Tris Hydrochloride, Polyethylene Glycol 8000, magnesium chloride, pH 8.5, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9801 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 12936 / Num. obs: 12379 / % possible obs: 95.7 % / Rmerge(I) obs: 0.13 / Χ2: 1.158 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible obs: 91.3 % / Rmerge(I) obs: 0.321 / Num. measured obs: 1132 / Χ2: 0.791 |
-Phasing
Phasing MR | Rfactor: 0.385 / Cor.coef. Fo:Fc: 0.66
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.879 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24 Å
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