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- PDB-7k2o: Kelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k2o | |||||||||
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Title | Kelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c[GABA-DPETGE] | |||||||||
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![]() | PROTEIN BINDING/Inhibitor / Peptide inhibitor / Inhibitor complex / Loop-mimic / PROTEIN BINDING / cyclic peptide / PROTEIN BINDING-Inhibitor complex | |||||||||
Function / homology | ![]() regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / 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 ...regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / 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 / disordered domain specific binding / KEAP1-NFE2L2 pathway / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Muellers, S.N. / Allen, K.N. | |||||||||
![]() | ![]() Title: Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. Authors: Ortet, P.C. / Muellers, S.N. / Viarengo-Baker, L.A. / Streu, K. / Szymczyna, B.R. / Beeler, A.B. / Allen, K.N. / Whitty, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266 KB | Display | ![]() |
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PDB format | ![]() | 190.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7k28C ![]() 7k29C ![]() 7k2aC ![]() 7k2bC ![]() 7k2cC ![]() 7k2dC ![]() 7k2eC ![]() 7k2fC ![]() 7k2gC ![]() 7k2hC ![]() 7k2iC ![]() 7k2jC ![]() 7k2kC ![]() 7k2lC ![]() 7k2mC ![]() 7k2nC ![]() 7k2pC ![]() 7k2qC ![]() 7k2rC ![]() 7k2sC ![]() 5wflS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 33122.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | ( | Mass: 731.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 1.2 - 1.5 M Ammonium Sulfate, 0.5-0.7% PEG-MME-550, 0.1 M Bis-Tris pH = 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.108→29.33 Å / Num. obs: 43354 / % possible obs: 99.27 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.71 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03772 / Rpim(I) all: 0.03772 / Rrim(I) all: 0.05335 / Net I/σ(I): 11.03 |
Reflection shell | Resolution: 2.108→2.183 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2884 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 4153 / CC1/2: 0.878 / CC star: 0.967 / Rpim(I) all: 0.2884 / Rrim(I) all: 0.4078 / % possible all: 95.75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WFL Resolution: 2.11→29.33 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8273 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: 56.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→29.33 Å
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Refine LS restraints |
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LS refinement shell |
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