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Yorodumi- PDB-4n1b: STRUCTURE OF KEAP1 KELCH DOMAIN WITH(1S,2R)-2-[(1S)-1-[(1-oxo-2,3... -
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-Basic information
Entry | Database: PDB / ID: 4n1b | ||||||
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Title | STRUCTURE OF KEAP1 KELCH DOMAIN WITH(1S,2R)-2-[(1S)-1-[(1-oxo-2,3-dihydro-1H-isoindol-2-Yl)methyl]-1,2,3,4-tetrahydroisoquinoline-2-Carbonyl]cyclohexane-1-carboxylic acid | ||||||
Components | Kelch-like ECH-associated protein 1 | ||||||
Keywords | TRANSCRIPTION/INHIBITOR / REPLACEMENT SOAKING / STRESS SENSOR / SMALL MOLECULAR BINDING / KELCH DOMAIN / KELCH REPEAT MOTIF / BETA-PROPELLER / NRF2 / PROTEIN-SMALL MOLECULE COMPLEX / CYTOSOL / TRANSCRIPTION-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Smith, M.A. / Duclos, S. / Beaumont, E. / Kwong, J. / Brooks, M. / Barker, J. / Jnoff, E. / Brookfield, F. / Courade, J.P. / Barker, O. ...Smith, M.A. / Duclos, S. / Beaumont, E. / Kwong, J. / Brooks, M. / Barker, J. / Jnoff, E. / Brookfield, F. / Courade, J.P. / Barker, O. / Fryatt, T. / Albrecht, C. / Bromidge, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n1b.cif.gz | 171.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n1b.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 4n1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n1b ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n1b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33009.801 Da / Num. of mol.: 3 / Fragment: ELCH DOMAIN, UNP RESIDUES 321-611 / Mutation: D354R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop 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 PH range: PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2012 / Details: mIRROR |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→32.68 Å / Num. all: 42242 / Num. obs: 42242 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 2.55 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→32.67 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / SU B: 15.005 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.316 / 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: 48.479 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→32.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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