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- PDB-5who: Kelch domain of human Keap1 bound to small molecule inhibitor fra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5who | ||||||
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Title | Kelch domain of human Keap1 bound to small molecule inhibitor fragment: 4-oxo-4H-1-benzopyran-2-carboxylic acid | ||||||
![]() | Kelch-like ECH-associated protein 1 | ||||||
![]() | TRANSCRIPTION/INHIBITOR / Scaffold / Inhibitor / Fragment / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | ![]() regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / 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 / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / midbody / cellular response to oxidative stress / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carolan, J.P. / Lynch, A.J. / Allen, K.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / ...Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / Vajda, S. / Allen, K.N. / Whitty, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
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Full document | ![]() | 483.7 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wflSC ![]() 5wfvC ![]() 5wg1C ![]() 5whlC ![]() 5wiyC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36899.176 Da / Num. of mol.: 2 / Mutation: E540A, E542A Source method: isolated from a genetically manipulated source Details: His-tagged variant including mutations for altered crystallographic packing Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AO7 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1.2 - 1.5 M Ammonium sulfate, 0.1 M Bis-Tris pH = 6.0 - 6.5 PH range: 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2014 Details: 12 V servo motors utilizing a CAMAC-based E500 stepper controller |
Radiation | Monochromator: Double crystals monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→51.85 Å / Num. obs: 37484 / % possible obs: 96.55 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.62 |
Reflection shell | Resolution: 2.23→2.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 3718 / CC1/2: 0.835 / % possible all: 89.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WFL Resolution: 2.23→51.848 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→51.848 Å
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Refine LS restraints |
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LS refinement shell |
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