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Yorodumi- PDB-2ys0: Solution structure of the Somatomedin B domain of human Ectonucle... -
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-Basic information
Entry | Database: PDB / ID: 2ys0 | ||||||
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Title | Solution structure of the Somatomedin B domain of human Ectonucleotide pyrophosphatase/phosphodiesterase family member | ||||||
Components | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 | ||||||
Keywords | HYDROLASE / E-NPP 1 / Phosphodiesterase I/nucleotide pyrophosphatase 1 / Plasma-cell membrane glycoprotein PC-1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 / sequestering of triglyceride / negative regulation of bone mineralization / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / 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 | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Abe, H. / Sasagawa, A. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the Somatomedin B domain of human Ectonucleotide pyrophosphatase/phosphodiesterase family member Authors: Abe, H. / Sasagawa, A. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 999 | SEQUENCE SWISSPROT shows that there is VARIANT AT THIS POSITION |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ys0.cif.gz | 294.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ys0.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ys0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/2ys0 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/2ys0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5841.409 Da / Num. of mol.: 1 / Fragment: somatomedin_B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: ENPP1 / Plasmid: P050118-03 References: UniProt: P22413, phosphodiesterase I, nucleotide diphosphatase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.80mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |