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Yorodumi- PDB-2l3h: NMR Structure in a Membrane Environment Reveals Putative Amyloido... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l3h | ||||||
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Title | NMR Structure in a Membrane Environment Reveals Putative Amyloidogenic Regions of the SEVI Precursor Peptide PAP248-286 | ||||||
Components | Prostatic acid phosphatase | ||||||
Keywords | HYDROLASE / SEVI / PAP248-286 | ||||||
Function / homology | Function and homology information thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / vesicle membrane / nucleotide metabolic process / choline binding / azurophil granule membrane / lysosome organization / phosphatase activity / purine nucleobase metabolic process / dephosphorylation / multivesicular body / protein-tyrosine-phosphatase / filopodium / protein tyrosine phosphatase activity / lipid metabolic process / apical part of cell / lysosome / molecular adaptor activity / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Ramamoorthy, A. / Nanga, R. / Brender, J. / Vivekanandan, S. / Popovych, N. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: NMR structure in a membrane environment reveals putative amyloidogenic regions of the SEVI precursor peptide PAP(248-286). Authors: Nanga, R.P. / Brender, J.R. / Vivekanandan, S. / Popovych, N. / Ramamoorthy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l3h.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l3h.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 2l3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/2l3h ftp://data.pdbj.org/pub/pdb/validation_reports/l3/2l3h | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4561.464 Da / Num. of mol.: 1 / Fragment: UNP residues 248-286 / Source method: obtained synthetically / Details: ACPP / Source: (synth.) Homo sapiens (human) / References: UniProt: P15309, acid phosphatase |
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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: 2.5 mM PAP248-286-1, 120 mM sodium chloride-2, 20 mM sodium phosphate-3, 200 mM [U-99% 2H] SDS-4, 10 % [U-99% 2H] D2O-5, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 / pH: 7.3 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 8 |