[English] 日本語
![](img/lk-miru.gif)
- PDB-8ejr: Kelch domain of human KEAP1 bound to Nrf2 linear peptide, Ac-GDPE... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ejr | ||||||
---|---|---|---|---|---|---|---|
Title | Kelch domain of human KEAP1 bound to Nrf2 linear peptide, Ac-GDPETGE-NH2 | ||||||
![]() |
| ||||||
![]() | PROTEIN BINDING / Protein interaction / inhibitor / cyclic peptide | ||||||
Function / homology | ![]() positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / non-membrane-bounded organelle / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / non-membrane-bounded organelle / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of cellular response to oxidative stress / negative regulation of vascular associated smooth muscle cell migration / regulation of removal of superoxide radicals / regulation of epidermal cell differentiation / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / positive regulation of ubiquitin-dependent protein catabolic process / mediator complex / NFE2L2 regulating inflammation associated genes / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / cellular response to angiotensin / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of cardiac muscle cell apoptotic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / NFE2L2 regulating tumorigenic genes / Cul3-RING ubiquitin ligase complex / proteasomal ubiquitin-independent protein catabolic process / regulation of innate immune response / regulation of embryonic development / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / cellular response to interleukin-4 / cellular response to glucose starvation / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / cell redox homeostasis / regulation of autophagy / transcription coregulator binding / response to ischemia / positive regulation of glucose import / actin filament / protein-DNA complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / KEAP1-NFE2L2 pathway / disordered domain specific binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Neddylation / midbody / cellular response to oxidative stress / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / Potential therapeutics for SARS / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / protein ubiquitination / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muellers, S.N. / Allen, K.N. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: The benefit of cyclization: a comparison of cyclic and linear peptide inhibitors of the KEAP1/Nrf2 protein-protein interaction Authors: Muellers, S.N. / Allen, K.N. / Whitty, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 134.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ejsC ![]() 5wfvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 36899.176 Da / Num. of mol.: 2 / Fragment: UNP residues 320-812 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 727.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1.6 M ammonium sulfate, 100 mM Bis-Tris pH 6.5, 0.8% PEG monomethyl ether (MME) 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→29.41 Å / Num. obs: 45416 / % possible obs: 98.96 % / Redundancy: 5 % / Biso Wilson estimate: 30.31 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.142 / Rrim(I) all: 0.318 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.08→2.154 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4519 / CC1/2: 0.77 / Rpim(I) all: 0.435 / Rrim(I) all: 0.99 / % possible all: 98.41 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5WFV Resolution: 2.08→29.41 Å / SU ML: 0.264 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.172 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→29.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|