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- PDB-4l7b: Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-1-[(1,3-dio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l7b | ||||||
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Title | Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-1-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid | ||||||
![]() | Kelch-like ECH-associated protein 1 | ||||||
![]() | TRANSCRIPTION/INHIBITOR / STRESS SENSOR / KELCH DOMAIN / KELCH REPEAT MOTIF / BETA-PROPELLER / NRF2 / PROTEIN-SMALL MOLECULE COMPLEX / 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 | ![]() ![]() ![]() | ||||||
![]() | Jnoff, E. / Brookfield, F. / Albrecht, C. / Barker, J.J. / Barker, O. / Beaumont, E. / Bromidge, S. / Brooks, M. / Ceska, T. / Courade, J.P. ...Jnoff, E. / Brookfield, F. / Albrecht, C. / Barker, J.J. / Barker, O. / Beaumont, E. / Bromidge, S. / Brooks, M. / Ceska, T. / Courade, J.P. / Crabbe, T. / Duclos, S. / Fryatt, T. / Jigorel, E. / Kwong, J. / Sands, Z. / Smith, M.A. | ||||||
![]() | ![]() Title: Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex. Authors: Jnoff, E. / Albrecht, C. / Barker, J.J. / Barker, O. / Beaumont, E. / Bromidge, S. / Brookfield, F. / Brooks, M. / Bubert, C. / Ceska, T. / Corden, V. / Dawson, G. / Duclos, S. / Fryatt, T. ...Authors: Jnoff, E. / Albrecht, C. / Barker, J.J. / Barker, O. / Beaumont, E. / Bromidge, S. / Brookfield, F. / Brooks, M. / Bubert, C. / Ceska, T. / Corden, V. / Dawson, G. / Duclos, S. / Fryatt, T. / Genicot, C. / Jigorel, E. / Kwong, J. / Maghames, R. / Mushi, I. / Pike, R. / Sands, Z.A. / Smith, M.A. / Stimson, C.C. / Courade, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 859.1 KB | Display | ![]() |
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Full document | ![]() | 861.2 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l7cC ![]() 4l7dC ![]() 4n1bC ![]() 1zgkS C: citing same article ( 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: 33009.801 Da / Num. of mol.: 2 / Fragment: Kelch domain, UNP residues 321-609 / Mutation: R354D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-1VV / ( | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.48 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1 ul of protein at 12 mg/ml in 20 mM Tris-HCl pH 7.5, 5 mM DTT, 5 mM compound 1 + 2 ul of 2.15 M Sodium Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012 / Details: Mirrors |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→75.37 Å / Num. all: 46220 / Num. obs: 46220 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 62.774 Å2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 2.41→2.47 Å / % possible all: 99.71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZGK Resolution: 2.41→60.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.271 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.371 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→60.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.473 Å / Total num. of bins used: 20
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