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- PDB-7xm3: Crystal structure of Keap1 Kelch domain (residues 322-609) in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xm3 | |||||||||
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Title | Crystal structure of Keap1 Kelch domain (residues 322-609) in complex with 6k | |||||||||
![]() | Kelch-like ECH-associated protein 1 | |||||||||
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Function / homology | ![]() negative regulation of response to oxidative stress / regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallography-Guided Optimizations of the Keap1-Nrf2 Inhibitors on the Solvent Exposed Region: From Symmetric to Asymmetric Naphthalenesulfonamides. Authors: Liu, G. / Hou, R. / Xu, L. / Zhang, X. / Yan, J. / Xing, C. / Xu, K. / Zhuang, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xm2C ![]() 7xm4C ![]() 7xm5C ![]() 4xmbS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 31936.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GED / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→50 Å / Num. obs: 11043 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.35 Å2 / Rmerge(I) obs: 0.278 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.8→2.89 Å / Rmerge(I) obs: 1.076 / Num. unique obs: 1055 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4XMB Resolution: 2.8→42.86 Å / SU ML: 0.3507 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.0155 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→42.86 Å
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Refine LS restraints |
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LS refinement shell |
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