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Open data
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Basic information
Entry | Database: PDB / ID: 8r6a | ||||||
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Title | DTX1 WWE domain in complex with ADP bound to WWE1 | ||||||
![]() | E3 ubiquitin-protein ligase DTX1 | ||||||
![]() | LIGASE / WWE domain | ||||||
Function / homology | ![]() negative regulation of T cell differentiation / regulation of Notch signaling pathway / glial cell differentiation / Notch binding / T cell differentiation / negative regulation of neuron differentiation / Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase ...negative regulation of T cell differentiation / regulation of Notch signaling pathway / glial cell differentiation / Notch binding / T cell differentiation / negative regulation of neuron differentiation / Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase / SH3 domain binding / ubiquitin protein ligase activity / transcription coactivator activity / transcription by RNA polymerase II / cell surface receptor signaling pathway / nuclear body / protein ubiquitination / DNA-templated transcription / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muenzker, L. / Zak, K.M. / Boettcher, J. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: A ligand discovery toolbox for the WWE domain family of human E3 ligases. Authors: Munzker, L. / Kimani, S.W. / Fowkes, M.M. / Dong, A. / Zheng, H. / Li, Y. / Dasovich, M. / Zak, K.M. / Leung, A.K.L. / Elkins, J.M. / Kessler, D. / Arrowsmith, C.H. / Halabelian, L. / Bottcher, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8r5nC ![]() 8r6bC ![]() 8r7oC ![]() 8rd0C ![]() 8rd1C ![]() 8rd7C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.999996780043, 0.00233841971642, 0.000985746729775), (-0.00233750537461, -0.999996837719, 0.000927696442905), (0.00098791295622, 0.000925389267484, 0.999999083841) ...NCS oper: (Code: given Matrix: (-0.999996780043, 0.00233841971642, 0.000985746729775), Vector: |
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Components
#1: Protein | Mass: 19400.014 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.0, 25 % v/v PEG MME 350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→68.68 Å / Num. obs: 15556 / % possible obs: 95.3 % / Redundancy: 2.25 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.25 |
Reflection shell | Resolution: 2.4→2.45 Å / Num. unique obs: 892 / CC1/2: 0.69 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→53.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.627279058513 Å | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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