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Yorodumi- PDB-8e07: Crystal structure of HPSE P6 in complex with triose pentosan inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 80000000 | ||||||
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Title | Crystal structure of HPSE P6 in complex with triose pentosan inhibitor | ||||||
Components |
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Keywords | HYDROLASE / Heparanase / Heparan Sulfate / Pentosan Polysulfate Sodium | ||||||
Function / homology | Function and homology information heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / beta-glucuronidase activity / heparan sulfate proteoglycan catabolic process / proteoglycan metabolic process / HS-GAG degradation / protein transmembrane transport / positive regulation of hair follicle development ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / beta-glucuronidase activity / heparan sulfate proteoglycan catabolic process / proteoglycan metabolic process / HS-GAG degradation / protein transmembrane transport / positive regulation of hair follicle development / 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 / extracellular matrix / lysosomal lumen / cell-matrix adhesion / response to organic substance / 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: 1.8 Å | ||||||
Authors | Whitefield, C. / Jackson, C.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Complex Inhibitory Mechanism of Glycomimetics with Heparanase. Authors: Whitefield, C. / Vo, Y. / Schwartz, B.D. / Hepburn, C. / Ahmed, F.H. / Onagi, H. / Banwell, M.G. / Nelms, K. / Malins, L.R. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e07.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e07.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 8e07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/8e07 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/8e07 | HTTPS FTP |
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-Related structure data
Related structure data | 8e08C 7rg8S C: citing same article (ref.) 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 AB
#1: Protein | Mass: 43375.863 Da / Num. of mol.: 1 Mutation: N178K, A195S, L197G, S212A, S219D, L230R, D234G, E244K, Q248H, R273G, S292A, R307L, I318T, S322Q, F327L, L354G, S426Q, K427D, K477Q, L483H, H486D, L498Q, M512K, E513P, S530A, A540P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251 |
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#2: Protein | Mass: 10267.545 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: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y251 |
-Sugars , 1 types, 2 molecules
#3: Polysaccharide | Type: oligosaccharide / Mass: 974.802 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 375 molecules
#4: Chemical | ChemComp-ACT / | ||||
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#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-NH4 / | #7: 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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M Ammonium Sulfate, Sodium Acetate pH 5.5, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.91 Å / Num. obs: 53337 / % possible obs: 99.6 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.097 / Χ2: 0.85 / Net I/σ(I): 14.8 / Num. measured all: 560186 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 97.1 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.944 / Num. measured all: 32591 / Num. unique obs: 3029 / CC1/2: 0.92 / Rpim(I) all: 0.299 / Rrim(I) all: 0.992 / Χ2: 0.47 / Net I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RG8 Resolution: 1.8→46.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.91 Å
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Refine LS restraints |
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LS refinement shell |
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