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Yorodumi- PDB-3s7s: Crystal structure of human placental aromatase complexed with bre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s7s | ||||||
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Title | Crystal structure of human placental aromatase complexed with breast cancer drug exemestane | ||||||
Components | Cytochrome P450 19A1 | ||||||
Keywords | Oxidoreductase/Oxidoreductase Inhibitor / Cytochrome P450 / Oxidoreductase / Oxidoreductase-Oxidoreductase Inhibitor complex | ||||||
Function / homology | Function and homology information aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / negative regulation of macrophage chemotaxis / mammary gland development / steroid biosynthetic process / steroid hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / aromatase activity / female gonad development / uterus development / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Ghosh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Novel aromatase inhibitors by structure-guided design. Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s7s.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s7s.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/3s7s ftp://data.pdbj.org/pub/pdb/validation_reports/s7/3s7s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57954.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP19A1, ARO1, CYAR, CYP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P11511, unspecific monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-EXM / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.86 Å3/Da / Density % sol: 79.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24-32% PEG 4000, phosphate buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.21→121.79 Å / Num. all: 22611 / Num. obs: 21353 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 106.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.93 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→121.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.375 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.35 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.385 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→121.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.21→3.291 Å / Total num. of bins used: 20
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