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- PDB-7k2g: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GDEEAGE] -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k2g | ||||||
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Title | Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[GDEEAGE] | ||||||
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![]() | PROTEIN BINDING/Inhibitor / Peptide inhibitor / ![]() ![]() ![]() | ||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 234.3 KB | Display | ![]() |
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PDB format | ![]() | 187.4 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 ![]() 7k2hC ![]() 7k2iC ![]() 7k2jC ![]() 7k2kC ![]() 7k2lC ![]() 7k2mC ![]() 7k2nC ![]() 7k2oC ![]() 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: 33005.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 705.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.09 % |
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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 PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→27.03 Å / Num. obs: 37540 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 46.78 Å2 / CC1/2: 1 / CC star: 0.926 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Rrim(I) all: 0.051 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.151→2.228 Å / Rmerge(I) obs: 0.551 / Num. unique obs: 2603 / CC1/2: 0.67 / CC star: 0.893 / Rpim(I) all: 0.663 / Rrim(I) all: 0.364 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5WFL Resolution: 2.15→27.03 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.64 / Stereochemistry target values: ML
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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 max: 131.12 Å2 / Biso mean: 46.777 Å2 / Biso min: 13.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→27.03 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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