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Yorodumi- PDB-2mzu: Extending the eNOE data set of large proteins by evaluation of NO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mzu | ||||||
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Title | Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals | ||||||
Components | Peptidyl-prolyl cis-trans isomerase A | ||||||
Keywords | ISOMERASE / Cyclophilin A | ||||||
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 | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | closest to the average, model20 | ||||||
Authors | Chi, C.N. / Strotz, D. / Riek, R. / Voegeli, B. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2015 Title: Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals. Authors: Chi, C.N. / Strotz, D. / Riek, R. / Vogeli, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mzu.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mzu.ent.gz | 953.2 KB | Display | PDB format |
PDBx/mmJSON format | 2mzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mzu_validation.pdf.gz | 477.9 KB | Display | wwPDB validaton report |
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Full document | 2mzu_full_validation.pdf.gz | 673.2 KB | Display | |
Data in XML | 2mzu_validation.xml.gz | 81.9 KB | Display | |
Data in CIF | 2mzu_validation.cif.gz | 90.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/2mzu ftp://data.pdbj.org/pub/pdb/validation_reports/mz/2mzu | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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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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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.5mm mM [U-100% 13C; U-100% 15N] sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.5 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 299 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software | Name: CYANA / Developer: Guntert P. / Classification: refinement |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 |