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Yorodumi- PDB-8b0c: Crystal structure of human heparanase in complex with covalent in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b0c | ||||||
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Title | Crystal structure of human heparanase in complex with covalent inhibitor VB158 | ||||||
Components |
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Keywords | HYDROLASE / Heparanase | ||||||
Function / homology | Function and homology information heparanase / heparanase activity / regulation of hair follicle development / heparan sulfate proteoglycan catabolic process / heparin metabolic process / proteoglycan metabolic process / HS-GAG degradation / positive regulation of hair follicle development / beta-glucuronidase activity / syndecan binding ...heparanase / heparanase activity / regulation of hair follicle development / heparan sulfate proteoglycan catabolic process / heparin metabolic process / proteoglycan metabolic process / HS-GAG degradation / positive regulation of hair follicle development / beta-glucuronidase activity / syndecan binding / protein transmembrane transport / 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 / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Armstrong, Z. / Davies, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chemmedchem / Year: 2023 Title: 4-O-Substituted Glucuronic Cyclophellitols are Selective Mechanism-Based Heparanase Inhibitors. Authors: Borlandelli, V. / Armstrong, Z. / Nin-Hill, A. / Codee, J.D.C. / Raich, L. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b0c.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b0c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8b0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b0c_validation.pdf.gz | 953.3 KB | Display | wwPDB validaton report |
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Full document | 8b0c_full_validation.pdf.gz | 957.6 KB | Display | |
Data in XML | 8b0c_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 8b0c_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/8b0c ftp://data.pdbj.org/pub/pdb/validation_reports/b0/8b0c | HTTPS FTP |
-Related structure data
Related structure data | 8b0bC 8b0dC 8b0eC 5e8mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43334.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251 | ||||||
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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.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251 | ||||||
#3: Sugar | #4: Chemical | ChemComp-OV3 / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52.71 Å / Num. obs: 29584 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2411 / CC1/2: 0.592 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5e8m Resolution: 2.1→52.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.182 / SU B: 7.793 / SU ML: 0.194 / Average fsc free: 0.8387 / Average fsc work: 0.8667 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.205 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: 47.328 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→52.71 Å
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Refine LS restraints |
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LS refinement shell |
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