+Open data
-Basic information
Entry | Database: PDB / ID: 8cqi | ||||||
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Title | Human heparanase in complex with inhibitor R3794 | ||||||
Components |
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Keywords | HYDROLASE / glycoside hydrolase / protein | ||||||
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 | Moran, E.M. / Davies, G.J. / Chen, C. / Nieuwendijk, E.V. / Wu, L. / Skoulikopoulou, F. / Riet, V.V. / Overkleeft, H.S. / Armstrong, Z. | ||||||
Funding support | European Union, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cqi.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cqi.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cqi_validation.pdf.gz | 914.7 KB | Display | wwPDB validaton report |
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Full document | 8cqi_full_validation.pdf.gz | 919.1 KB | Display | |
Data in XML | 8cqi_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8cqi_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqi ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqi | HTTPS FTP |
-Related structure data
Related structure data | 8ogxC 8ohqC 8ohrC 8ohtC 8ohuC 8ohvC 8ohwC 8ohxC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43733.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DPG 155-157 expression tag / 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: 8542.769 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, heparanase |
-Sugars , 1 types, 5 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 142 molecules
#4: Chemical | ChemComp-VGO / ( | ||||||
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#5: Chemical | #6: Chemical | ChemComp-LYY / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % |
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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, 0.1M magnesium chloride, 18% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.61 Å / Num. obs: 30450 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.99 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 2452 / CC1/2: 0.42 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.071 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.196 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.776 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→46.61 Å
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