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- PDB-1nd6: Crystal Structures of Human Prostatic Acid Phosphatase in Complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nd6 | |||||||||
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Title | Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design | |||||||||
![]() | prostatic acid phosphatase | |||||||||
![]() | HYDROLASE / Prostatic acid Phosphatase / PAP / Prostate / Phosphate / inhibitor | |||||||||
Function / homology | ![]() 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 / XMP 5'-nucleosidase activity / acid phosphatase 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 / XMP 5'-nucleosidase activity / acid phosphatase 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 / protein tyrosine phosphatase activity / filopodium / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ortlund, E. / LaCount, M.W. / Lebioda, L. | |||||||||
![]() | ![]() Title: Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and alpha-benzylaminobenzylphosphonic acid update the mechanistic picture and offer new insights into inhibitor design Authors: Ortlund, E. / LaCount, M.W. / Lebioda, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.4 KB | Display | ![]() |
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PDB format | ![]() | 248.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 852.9 KB | Display | ![]() |
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Full document | ![]() | 900.1 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Details | The Biological Assembley is a dimer. The asymmetric unit contains two such dimers. |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41050.602 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 6 types, 7 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
#5: 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 |
#6: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-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 |
#9: Sugar |
-Non-polymers , 4 types, 473 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-PO4 / #8: Chemical | ChemComp-1PE / #10: Chemical | ChemComp-GLY / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.22 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10 Details: PEG, KCL, Glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. all: 89003 / Num. obs: 89003 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.9 Å2 |
Reflection shell | Resolution: 2.36→2.47 Å / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 99.8 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.317 Å2 / ksol: 0.344379 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.36 Å / Luzzati sigma a free: 0.33 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→35.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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