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- PDB-1nd5: 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: 1nd5 | |||||||||
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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 / 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 / filopodium / protein tyrosine phosphatase activity / 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 | ![]() | 298.7 KB | Display | ![]() |
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PDB format | ![]() | 242.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 59.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nd6C ![]() 2hpaS S: Starting model for refinement C: citing same article ( |
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Similar 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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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 , 4 types, 7 molecules ![](data/chem/img/NDG.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: 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 #3: 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: Sugar | ChemComp-NDG / | #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 147 molecules ![](data/chem/img/2BF.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-2BF / #5: Chemical | ChemComp-1PE / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 / Details: Yale Mirrors |
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: 2.89→50 Å / Num. all: 33191 / Num. obs: 33191 / % possible obs: 82.2 % / Biso Wilson estimate: 74.4 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.89→3 Å / % possible all: 63.7 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS Lowest resolution: 3 Å / % possible obs: 63.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2hpa Resolution: 2.9→77.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 245501.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.2524 Å2 / ksol: 0.354636 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze | Luzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.5 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→77.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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