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Open data
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Basic information
Entry | Database: PDB / ID: 5la4 | |||||||||||||||
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Title | Crystal structure of apo human proheparanase | |||||||||||||||
![]() | Heparanase | |||||||||||||||
![]() | HYDROLASE / heparanase / proenzyme / GH79 | |||||||||||||||
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 / syndecan binding ...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 / 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 / extracellular matrix / cell-matrix adhesion / 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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Wu, L. / Jin, Y. / Davies, G.J. | |||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Activity-based probes for functional interrogation of retaining beta-glucuronidases. Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / ...Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / Overkleeft, H.S. / Davies, G.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126 KB | Display | ![]() |
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PDB format | ![]() | 93.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5g0qC ![]() 5l77C ![]() 5l9yC ![]() 5l9zC ![]() 5la7C ![]() 5e8mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57725.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar |
-Non-polymers , 2 types, 223 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1 M Succinate pH 7.0 17% PEG3350 1:250 dilution seed stock - Seed stock grown in 0.2M Ammonium Nitrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.58 Å / Num. obs: 43065 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.3 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E8M Resolution: 1.9→46.58 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.767 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.878 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→46.58 Å
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Refine LS restraints |
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