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Yorodumi- PDB-5ovr: X-Ray Characterization of Striatal-Enriched Protein Tyrosine Phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ovr | ||||||
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Title | X-Ray Characterization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 5 | ||||||
Keywords | HYDROLASE / Phosphatase Alzheimer's disease Inhibitor STEP | ||||||
Function / homology | Function and homology information Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Kack, H. / Wissler, L. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: X-ray Characterization and Structure-Based Optimization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors. Authors: Witten, M.R. / Wissler, L. / Snow, M. / Geschwindner, S. / Read, J.A. / Brandon, N.J. / Nairn, A.C. / Lombroso, P.J. / Kack, H. / Ellman, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ovr.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ovr.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 5ovr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ovr_validation.pdf.gz | 735.8 KB | Display | wwPDB validaton report |
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Full document | 5ovr_full_validation.pdf.gz | 735.8 KB | Display | |
Data in XML | 5ovr_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5ovr_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovr ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovr | HTTPS FTP |
-Related structure data
Related structure data | 5ovxC 5ow1C 2bv5S S: Starting model for refinement C: citing same article (ref.) |
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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: 35220.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN5 / Production host: Escherichia coli (E. coli) / References: UniProt: P54829, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-AXK / [(~{ |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 26-28% PEG3350, 0.1M Bis-Tris pH5.5, 0.2M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100.43 Å / Num. obs: 19180 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 20.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.053 / Rrim(I) all: 0.141 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.765 / Num. unique obs: 1549 / CC1/2: 0.928 / Rpim(I) all: 0.312 / Rrim(I) all: 0.827 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BV5 Resolution: 2.15→21.69 Å / Cor.coef. Fo:Fc: 0.9065 / Cor.coef. Fo:Fc free: 0.8383 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.338 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.237
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Displacement parameters | Biso max: 108.11 Å2 / Biso mean: 17.17 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.277 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→21.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.27 Å / Rfactor Rfree error: 0
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