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Yorodumi- PDB-5dad: Crystal Structure of Human KEAP1 BTB Domain in Complex with Small... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dad | ||||||
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Title | Crystal Structure of Human KEAP1 BTB Domain in Complex with Small Molecule TX64014 | ||||||
Components | Kelch-like ECH-associated protein 1 | ||||||
Keywords | TRANSCRIPTION / KEAP1 / Trascription Regulation / BTB domain / Cysteine Modification / C1-(R)-Cys151 adduct | ||||||
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: 2.61 Å | ||||||
Authors | Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. ...Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. / Visnick, M. / Wigley, W.C. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2016 Title: Characterization of novel small-molecule NRF2 activators: Structural and biochemical validation of stereospecific KEAP1 binding. Authors: Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Ferguson, D.A. / Probst, B. / Swinger, K.K. / Stoll, V.S. / Thomas, P.J. / Dulubova, I. / Visnick, M. / Wigley, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dad.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dad.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5dad ftp://data.pdbj.org/pub/pdb/validation_reports/da/5dad | HTTPS FTP |
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-Related structure data
Related structure data | 5dafSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15594.950 Da / Num. of mol.: 1 / Fragment: BTB domain, residues 49-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q14145 |
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#2: Chemical | ChemComp-TX6 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium Thiocyanate, 30% w/v PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 / Details: Pixel | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.605→135.171 Å / Num. obs: 4678 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 32 / Num. measured all: 44180 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DAF Resolution: 2.61→45.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2442 / WRfactor Rwork: 0.1975 / FOM work R set: 0.7795 / SU B: 12.836 / SU ML: 0.256 / SU R Cruickshank DPI: 0.7813 / SU Rfree: 0.3063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.781 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 102.91 Å2 / Biso mean: 63.438 Å2 / Biso min: 41.99 Å2
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Refinement step | Cycle: final / Resolution: 2.61→45.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.605→2.673 Å / Total num. of bins used: 20
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