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Yorodumi- PDB-6weu: Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6weu | ||||||
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Title | Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate | ||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / human E-NPP 1 / drug discovery / inhibitors / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism ...GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism / nucleoside triphosphate catabolic process / nucleotide diphosphatase / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / intracellular phosphate ion homeostasis / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / nucleic acid metabolic process / sequestering of triglyceride / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / negative regulation of bone mineralization / phosphate ion homeostasis / melanocyte differentiation / phosphodiesterase I activity / scavenger receptor activity / negative regulation of glucose import / regulation of bone mineralization / phosphate-containing compound metabolic process / exonuclease activity / negative regulation of fat cell differentiation / polysaccharide binding / response to ATP / bone mineralization / phosphatase activity / 3',5'-cyclic-AMP phosphodiesterase activity / response to inorganic substance / ATP metabolic process / negative regulation of insulin receptor signaling pathway / generation of precursor metabolites and energy / insulin receptor binding / negative regulation of cell growth / cellular response to insulin stimulus / gene expression / basolateral plasma membrane / nucleic acid binding / immune response / lysosomal membrane / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / zinc ion binding / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Peat, T.S. / Dennis, M. / Newman, J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Crystal structures of human ENPP1 in apo and bound forms. Authors: Dennis, M.L. / Newman, J. / Dolezal, O. / Hattarki, M. / Surjadi, R.N. / Nuttall, S.D. / Pham, T. / Nebl, T. / Camerino, M. / Khoo, P.S. / Monahan, B.J. / Peat, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6weu.cif.gz | 356.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6weu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6weu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6weu ftp://data.pdbj.org/pub/pdb/validation_reports/we/6weu | HTTPS FTP |
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-Related structure data
Related structure data | 6wetSC 6wevC 6wewC 6wfjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AbABbB
#1: Protein | Mass: 105058.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP1, M6S1, NPPS, PC1, PDNP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: P22413, phosphodiesterase I, nucleotide diphosphatase |
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-Sugars , 4 types, 9 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 | Source method: isolated from a genetically manipulated source #4: 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 #6: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 129 molecules
#5: Chemical | ChemComp-ZN / #7: Chemical | #8: Chemical | ChemComp-EDO / | #9: 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: 3.32 Å3/Da / Density % sol: 62.9 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate |
-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: 0.953731 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953731 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→47.613 Å / Num. obs: 82015 / % possible obs: 100 % / Redundancy: 26.9 % / CC1/2: 0.997 / Rpim(I) all: 0.055 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.65→2.7 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4439 / CC1/2: 0.508 / Rpim(I) all: 0.816 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6WET Resolution: 2.65→47.57 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.139 / SU ML: 0.219 / Cross valid method: FREE R-VALUE / ESU R: 0.402 / ESU R Free: 0.265 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: 60.145 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→47.57 Å
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Refine LS restraints |
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LS refinement shell |
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