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- PDB-8ohr: Crystal structure of human heparanase in complex with glucuronic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ohr | |||||||||||||||||||||
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Title | Crystal structure of human heparanase in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor | |||||||||||||||||||||
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![]() | HYDROLASE / Inhibitor / Complex | |||||||||||||||||||||
Function / homology | ![]() heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport / syndecan binding / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / lysosomal lumen / cell-matrix adhesion / : / extracellular matrix / specific granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Armstrong, Z. / Yurong, C. / Wu, L. / Overkleeft, H.S. / Davies, G.J. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B. Authors: Chen, Y. / van den Nieuwendijk, A.M.C.H. / Wu, L. / Moran, E. / Skoulikopoulou, F. / van Riet, V. / Overkleeft, H.S. / Davies, G.J. / Armstrong, Z. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 861.1 KB | Display | ![]() |
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Full document | ![]() | 864.8 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cqiC ![]() 8ogxC ![]() 8ohqC ![]() 8ohtC ![]() 8ohuC ![]() 8ohvC ![]() 8ohwC ![]() 8ohxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 43334.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 8273.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/NAG.gif)
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 187 molecules ![](data/chem/img/VP5.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-VP5 / ( | ||||
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#4: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979499 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.994 Å / Num. obs: 44493 / % possible obs: 99.1 % / Redundancy: 4.6 % / CC1/2: 0.993 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2569 / CC1/2: 0.606 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.174 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.994 Å
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Refine LS restraints |
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LS refinement shell |
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