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Yorodumi- PDB-1w8m: Enzymatic and Structural Characterisation of Non Peptide Ligand C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8m | ||||||
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Title | Enzymatic and Structural Characterisation 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 / viral release from host cell / Calcineurin activates NFAT / protein peptidyl-prolyl isomerization / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 1w8m.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8m.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1w8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w8m_validation.pdf.gz | 379.8 KB | Display | wwPDB validaton report |
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Full document | 1w8m_full_validation.pdf.gz | 384.4 KB | Display | |
Data in XML | 1w8m_validation.xml.gz | 6 KB | Display | |
Data in CIF | 1w8m_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8m ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8m | HTTPS FTP |
-Related structure data
Related structure data | 1w8lC 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-E1P / |
#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: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH 300 / Detector: IMAGE PLATE / Date: Aug 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24 Å / Num. obs: 17641 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 10 / % possible all: 86.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CWH Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.779 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
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Refine LS restraints |
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