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Yorodumi- PDB-8e08: Crystal structure of HPSE P6 in complex with tetraose pentosan in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 800000000 | ||||||
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Title | Crystal structure of HPSE P6 in complex with tetraose pentosan inhibitor | ||||||
Components |
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Keywords | HYDROLASE / Heparanase / Heparan Sulfate | ||||||
Function / homology | Function and homology information 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 / protein transmembrane transport ...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 / protein transmembrane transport / 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 / lysosomal lumen / cell-matrix adhesion / : / extracellular matrix / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 | 8e08.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e08.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 8e08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e08_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8e08_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8e08_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 8e08_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/8e08 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/8e08 | HTTPS FTP |
-Related structure data
Related structure data | 8e07C 7rg8S 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
-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, 3 molecules
#3: Polysaccharide | Type: oligosaccharide / Mass: 1267.042 Da / Num. of mol.: 3 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 314 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-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: 2.59 Å3/Da / Density % sol: 52.59 % |
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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: Dec 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→48.28 Å / Num. obs: 43216 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 0.75 / Net I/σ(I): 11.8 / Num. measured all: 561577 |
Reflection shell | Resolution: 1.93→1.98 Å / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.925 / Num. measured all: 38828 / Num. unique obs: 2843 / CC1/2: 0.938 / Rpim(I) all: 0.257 / Rrim(I) all: 0.96 / Χ2: 0.39 / Net I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RG8 Resolution: 1.93→48.28 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.21 / 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: 1.93→48.28 Å
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Refine LS restraints |
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LS refinement shell |
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