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- PDB-6lcb: Crystal structure of human Dishevelled1 PDZ domain with its inhib... -
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Basic information
Entry | Database: PDB / ID: 6lcb | ||||||
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Title | Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009 | ||||||
![]() | Segment polarity protein dishevelled homolog DVL-1 | ||||||
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Function / homology | ![]() positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / protein localization to microtubule / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / presynapse assembly ...positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / protein localization to microtubule / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / presynapse assembly / collateral sprouting / WNT5:FZD7-mediated leishmania damping / neurotransmitter secretion / dendritic spine morphogenesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H. | ||||||
![]() | ![]() Title: Crystal structure of human Dishevelled1 PDZ domain with its inhibitor NPL3009 Authors: Yasukochi, S. / Numoto, N. / Tenno, N. / Tenno, T. / Ito, N. / Hiroaki, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.1 KB | Display | ![]() |
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PDB format | ![]() | 21.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6lcaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10771.055 Da / Num. of mol.: 1 / Mutation: C338A,W339T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-E83 / |
#3: Chemical | ChemComp-SO4 / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate tribasic dehydrate 1.0 M Lithium sulfate monohydrate 1.0 M Guanidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→50 Å / Num. obs: 17013 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 21.45 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.4→1.47 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2661 / CC1/2: 0.861 / Rsym value: 0.882 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6LCA Resolution: 1.4→40.6 Å / SU ML: 0.1626 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2392
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→40.6 Å
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Refine LS restraints |
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LS refinement shell |
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