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Open data
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Basic information
Entry | Database: PDB / ID: 7xot | |||||||||
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Title | Crystal structure of Keap1_6k | |||||||||
![]() | Kelch-like ECH-associated protein 1 | |||||||||
![]() | PROTEIN BINDING / oxidative stress sensor | |||||||||
Function / homology | ![]() regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / disordered domain specific binding / KEAP1-NFE2L2 pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Keap1_6k Authors: Xu, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xmbS S: Starting model for refinement |
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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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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-HB6 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.01 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4.0M Ammonium acetate, 0.1M Tris-HCl, pH 8.8. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 12109 / % possible obs: 98.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 39.89 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 1198 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XMB Resolution: 2.7→24.94 Å / SU ML: 0.3435 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9261 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: 38.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→24.94 Å
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Refine LS restraints |
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LS refinement shell |
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