+Open data
-Basic information
Entry | Database: PDB / ID: 8q1r | ||||||||||||||||||
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Title | mouse Keap1 in complex with stapled peptide | ||||||||||||||||||
Components |
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Keywords | LIGASE / Keap1 / cyclic peptide / E3 ligase adaptor / antioxidant response | ||||||||||||||||||
Function / homology | Function and homology information cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / 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 / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / negative regulation of gene expression / focal adhesion / regulation of DNA-templated transcription / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||||||||||||||
Authors | Kack, H. / Wissler, L. | ||||||||||||||||||
Funding support | Sweden, United Kingdom, Czech Republic, 5items
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Citation | Journal: Chem Sci / Year: 2023 Title: A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction. Authors: Iegre, J. / Krajcovicova, S. / Gunnarsson, A. / Wissler, L. / Kack, H. / Luchniak, A. / Tangefjord, S. / Narjes, F. / Spring, D.R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q1r.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q1r.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 8q1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1r ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1r | HTTPS FTP |
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-Related structure data
Related structure data | 8q1qC 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
-Protein / Protein/peptide , 2 types, 2 molecules AE
#1: Protein | Mass: 33305.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X8 |
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#2: Protein/peptide | Mass: 990.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 280 molecules
#3: Chemical | ChemComp-SO4 / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-IZS / |
#6: Water | ChemComp-HOH / |
-Details
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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.9 Details: 0.7-0.9M Lithium Sulfate, 0.5-0.7M Ammonium sulfate and 0.1M Sodium Citrate pH5.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→89.234 Å / Num. obs: 523089 / % possible obs: 88.3 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.33→1.43 Å / Rmerge(I) obs: 0.762 / Num. unique obs: 2656 / CC1/2: 0.571 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→19.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.061
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Displacement parameters | Biso mean: 31.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→19.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.34 Å
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Refinement TLS params. | Origin x: -90.1115 Å / Origin y: 100.689 Å / Origin z: -3.084 Å
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Refinement TLS group |
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