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Yorodumi- PDB-1w8l: Enzymatic and structural characterization of non peptide ligand c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8l | ||||||
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Title | Enzymatic and structural characterization of non peptide ligand cyclophilin complexes | ||||||
Components | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A | ||||||
Keywords | ISOMERASE / COMPLEX (ISOMERASE-IMMUNOSUPPRESSANT) / NON-PEPTIDE LIGAND / MULTIGENE FAMILY / ROTAMASE | ||||||
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 / virion binding / leukocyte chemotaxis / 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 / 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 / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / 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 / 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 / platelet aggregation / integrin binding / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein 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 / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / 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: 1.8 Å | ||||||
Authors | Kontopidis, G. / Taylor, P. / Walkinshaw, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Enzymatic and Structural Characterization of Non-Peptide Ligand-Cyclophilin Complexes Authors: Kontopidis, G. / Taylor, P. / Walkinshaw, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w8l.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8l.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w8l_validation.pdf.gz | 379.4 KB | Display | wwPDB validaton report |
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Full document | 1w8l_full_validation.pdf.gz | 382.4 KB | Display | |
Data in XML | 1w8l_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1w8l_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8l ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8l | HTTPS FTP |
-Related structure data
Related structure data | 1w8mC 1w8vC 1cwhS 1w7y C: citing same article (ref.) 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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-1P3 / ( |
#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: 1.9 Å3/Da / Density % sol: 36.2 % |
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Crystal grow | pH: 8 Details: 100MM TRIS.HCL (PH 8.0), 22% (W/V) PEG 8000, 5% (V/V) DMSO, 0.02% NAN3. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH 300 / Detector: IMAGE PLATE / Date: Jan 10, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24 Å / Num. obs: 13305 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.5 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CWH Resolution: 1.8→24 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ALTERNATIVE CONFORMATION ARG 55
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Refinement step | Cycle: LAST / Resolution: 1.8→24 Å
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Refine LS restraints |
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