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Yorodumi- PDB-2ylo: TARGETING THE BINDING FUNCTION 3 SITE OF THE ANDROGEN RECEPTOR TH... -
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-Basic information
Entry | Database: PDB / ID: 2ylo | ||||||
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Title | TARGETING THE BINDING FUNCTION 3 SITE OF THE ANDROGEN RECEPTOR THROUGH IN SILICO MOLECULAR MODELING | ||||||
Components | ANDROGEN RECEPTOR | ||||||
Keywords | HORMONE RECEPTOR / BINDING FUNCTION 3 | ||||||
Function / homology | Function and homology information male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation ...male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / non-membrane-bounded organelle assembly / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / intracellular receptor signaling pathway / cellular response to testosterone stimulus / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / positive regulation of intracellular estrogen receptor signaling pathway / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / molecular condensate scaffold activity / epithelial cell proliferation / G protein-coupled receptor activity / positive regulation of cell differentiation / negative regulation of extrinsic apoptotic signaling pathway / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lack, N.A. / Axerio, P. / Tavassoli, P. / Kuchenbecker, K. / Han, F.Q. / Chan, K.H. / Feau, C. / LeBlanc, E. / Tomlinson, E. / Guy, R.K. ...Lack, N.A. / Axerio, P. / Tavassoli, P. / Kuchenbecker, K. / Han, F.Q. / Chan, K.H. / Feau, C. / LeBlanc, E. / Tomlinson, E. / Guy, R.K. / Rennie, P.S. / Cherkasov, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Targeting the Binding Function 3 (Bf3) Site of the Human Androgen Receptor Through Virtual Screening. Authors: Lack, N.A. / Axerio-Cilies, P. / Tavassoli, P. / Han, F.Q. / Chan, K.H. / Feau, C. / Leblanc, E. / Guns, E.T. / Guy, R.K. / Rennie, P.S. / Cherkasov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ylo.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ylo.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ylo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ylo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2ylo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ylo_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2ylo_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2ylo ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2ylo | HTTPS FTP |
-Related structure data
Related structure data | 2ylpC 2ylqC 3zqtC 2am9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 29868.949 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 664-919 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10275 |
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#2: Chemical | ChemComp-TES / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-YLO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: ASYMMETRIC CUT SINGLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.2 Å / Num. obs: 9822 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AM9 Resolution: 2.5→49.2 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.248 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.998 / ESU R Free: 0.353 / 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: 40.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→49.2 Å
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