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Yorodumi- PDB-5hpw: Mode of binding of antithyroid drug, propylthiouracil to lactoper... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hpw | |||||||||
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Title | Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / calcium ion binding / heme binding / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Capra hircus (goat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Singh, R.P. / Singh, A. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To Be Published Title: Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination Authors: Singh, R.P. / Singh, A. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hpw.cif.gz | 495.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hpw.ent.gz | 408.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hpw_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5hpw_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 5hpw_validation.xml.gz | 112.1 KB | Display | |
Data in CIF | 5hpw_validation.cif.gz | 147.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpw ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpw | HTTPS FTP |
-Related structure data
Related structure data | 4ljj S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 67529.781 Da / Num. of mol.: 4 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS |
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-Sugars , 3 types, 11 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 675 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-NO3 / #7: Chemical | ChemComp-3CJ / #8: Chemical | ChemComp-HEM / #9: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2M Ammonium nitrate, 30% PEG 3350, pH 6.2 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 9, 2014 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.5 Å / Num. obs: 73405 / % possible obs: 93 % / Redundancy: 2 % / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.503→2.568 Å / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LJJ 4ljj Resolution: 2.5→42.5 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.422 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42.5 Å
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Refine LS restraints |
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