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Yorodumi- PDB-8bac: Crystal structure of human heparanase in complex with competitive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bac | ||||||
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Title | Crystal structure of human heparanase in complex with competitive inhibitor GD05 | ||||||
Components |
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Keywords | HYDROLASE / inhibitor complex | ||||||
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: 2.05 Å | ||||||
Authors | Armstrong, Z. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: Synthesis of Uronic Acid 1-Azasugars as Putative Inhibitors of alpha-Iduronidase, beta-Glucuronidase and Heparanase. Authors: Doherty, G.G. / Ler, G.J.M. / Wimmer, N. / Bernhardt, P.V. / Ashmus, R.A. / Vocadlo, D.J. / Armstrong, Z. / Davies, G.J. / Maccarana, M. / Li, J.P. / Kayal, Y. / Ferro, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bac.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bac.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bac_validation.pdf.gz | 845.2 KB | Display | wwPDB validaton report |
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Full document | 8bac_full_validation.pdf.gz | 851.6 KB | Display | |
Data in XML | 8bac_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 8bac_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/8bac ftp://data.pdbj.org/pub/pdb/validation_reports/ba/8bac | HTTPS FTP |
-Related structure data
Related structure data | 7prtS S: Starting model for refinement |
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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
-Protein , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 43733.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Heparanase 50 kDa subunit / 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 |
-Sugars , 1 types, 2 molecules
#3: Sugar |
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-Non-polymers , 3 types, 96 molecules
#4: Chemical | ChemComp-EDO / |
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#5: Chemical | ChemComp-SJ5 / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.39 Å3/Da / Density % sol: 48.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→37.677 Å / Num. obs: 30692 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.05→2.11 Å / Num. unique obs: 2345 / CC1/2: 0.672 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PRT Resolution: 2.05→37.677 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.221 / SU B: 8.489 / SU ML: 0.214 / Average fsc free: 0.7967 / Average fsc work: 0.8169 / Cross valid method: FREE R-VALUE / ESU R: 0.241 / ESU R Free: 0.2 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: 45.913 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→37.677 Å
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Refine LS restraints |
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LS refinement shell |
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