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Yorodumi- PDB-7xm4: Crystal structure of Keap1 Kelch domain (residues 322-609) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xm4 | |||||||||
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Title | Crystal structure of Keap1 Kelch domain (residues 322-609) in complex with 6e | |||||||||
Components | Kelch-like ECH-associated protein 1 | |||||||||
Keywords | PROTEIN BINDING / oxidative stress sensor | |||||||||
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: 2.7 Å | |||||||||
Authors | Xu, K. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Crystallography-Guided Optimizations of the Keap1-Nrf2 Inhibitors on the Solvent Exposed Region: From Symmetric to Asymmetric Naphthalenesulfonamides. Authors: Liu, G. / Hou, R. / Xu, L. / Zhang, X. / Yan, J. / Xing, C. / Xu, K. / Zhuang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xm4.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xm4.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/7xm4 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/7xm4 | HTTPS FTP |
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-Related structure data
Related structure data | 7xm2C 7xm3C 7xm5C 4xmbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31936.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145 |
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#2: Chemical | ChemComp-GDJ / |
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: 3.51 Å3/Da / Density % sol: 64.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 12192 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.08 Å2 / Rmerge(I) obs: 0.228 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 1.159 / Num. unique obs: 1210 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XMB Resolution: 2.7→42.78 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2539 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→42.78 Å
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Refine LS restraints |
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LS refinement shell |
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