+Open data
-Basic information
Entry | Database: PDB / ID: 6tym | ||||||
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Title | KEAP1 Kelch domain in complex with Compound 9 | ||||||
Components | Kelch-like ECH-associated protein 1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / Keap1 Kelch domain | ||||||
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: 1.422 Å | ||||||
Authors | Marcotte, D.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 Title: Design, synthesis and identification of novel, orally bioavailable non-covalent Nrf2 activators. Authors: Ma, B. / Lucas, B. / Capacci, A. / Lin, E.Y. / Jones, J.H. / Dechantsreiter, M. / Enyedy, I. / Marcotte, D. / Xiao, G. / Li, B. / Richter, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tym.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tym.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/6tym ftp://data.pdbj.org/pub/pdb/validation_reports/ty/6tym | HTTPS FTP |
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-Related structure data
Related structure data | 6typC 4iqkS 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
#1: Protein | Mass: 32067.844 Da / Num. of mol.: 1 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 | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.9M ammonium citrate and 100mM HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.422→19.308 Å / Num. obs: 53482 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.422→1.5 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7662 / CC1/2: 0.43 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IQK Resolution: 1.422→19.308 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 61.66 Å2 / Biso mean: 12.8191 Å2 / Biso min: 3.92 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.422→19.308 Å
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