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Open data
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Basic information
Entry | Database: PDB / ID: 6pya | ||||||
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Title | Sex Hormone-binding globulin mutant E176K in complex with IPI | ||||||
![]() | Sex hormone-binding globulin | ||||||
![]() | HORMONE / Sex Steroid Transport Binding Globulin | ||||||
Function / homology | ![]() androgen binding / steroid binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Round, P.W. / Das, S. / Van Petegem, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular interactions between sex hormone-binding globulin and nonsteroidal ligands that enhance androgen activity. Authors: Round, P. / Das, S. / Wu, T.S. / Wahala, K. / Van Petegem, F. / Hammond, G.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 | ![]() | 51.6 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.2 KB | Display | ![]() |
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Full document | ![]() | 786 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22610.689 Da / Num. of mol.: 1 / Mutation: E176K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-P57 / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % / Description: Crystals were diamond shaped |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% Peg 3350, 0.2 M potassium thiocyanate, HEPES pH 7.5, 2.5 mM Calcium Chloride Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2016 | ||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.71→26.12 Å / Num. obs: 23105 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2 / Num. measured all: 277976 / Scaling rejects: 173 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.5 Å2 / Biso mean: 32.5125 Å2 / Biso min: 14.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→26.12 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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