+Open data
-Basic information
Entry | Database: PDB / ID: 6z6a | |||||||||
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Title | Keap1 macrocycle complex | |||||||||
Components | Kelch-like ECH-associated protein 1 | |||||||||
Keywords | LIGASE / macrocycle / complex | |||||||||
Function / homology | Function and homology information negative regulation of response to oxidative stress / regulation of epidermal cell differentiation / 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 response to oxidative stress / regulation of epidermal cell differentiation / 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 / KEAP1-NFE2L2 pathway / disordered domain specific binding / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å | |||||||||
Authors | Johansson, P. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Mining Natural Products for Macrocycles to Drug Difficult Targets. Authors: Begnini, F. / Poongavanam, V. / Over, B. / Castaldo, M. / Geschwindner, S. / Johansson, P. / Tyagi, M. / Tyrchan, C. / Wissler, L. / Sjo, P. / Schiesser, S. / Kihlberg, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z6a.cif.gz | 237.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z6a.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/6z6a ftp://data.pdbj.org/pub/pdb/validation_reports/z6/6z6a | HTTPS FTP |
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-Related structure data
Related structure data | 1zgkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32064.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14145 #2: Chemical | ChemComp-Q9E / ( | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.54 Å3/Da / Density % sol: 72.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 nL of protein (11-13 mg / mL) and 200 nL of well solution (3.7 to 4.1 M ammonium acetate, 0.09 M sodium acetate pH 4.6 and 10 mM cadmium chloride). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.37→47.37 Å / Num. obs: 48272 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 80.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Net I/σ(I): 15.4 / Num. measured all: 312117 / Scaling rejects: 43 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZGK Resolution: 2.37→47.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso max: 151.36 Å2 / Biso mean: 70 Å2 / Biso min: 46.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.37→47.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.43 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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