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- PDB-9ih9: KEAP1 complexed to linear peptide 6 -

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Basic information

Entry
Database: PDB / ID: 9ih9
TitleKEAP1 complexed to linear peptide 6
Components
  • (Kelch-like ECH-associated protein ...) x 3
  • Designed peptide
KeywordsSTRUCTURAL PROTEIN / Cyclic peptide / Protein-protein interaction
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / transcription regulator inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / transcription regulator inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / centriolar satellite / disordered domain specific binding / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / cellular response to oxidative stress / midbody / Potential therapeutics for SARS / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein ubiquitination / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / DI(HYDROXYETHYL)ETHER / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXinjian, J. / Kelvin, L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: De novo generation of a membrane-permeable cyclic peptides that target an intracellular protein-protein interaction
Authors: Xinjian, J. / Kelvin, L.
History
DepositionFeb 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
A: Kelch-like ECH-associated protein 1
X: Designed peptide
Y: Designed peptide
Z: Designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,92126
Polymers96,5836
Non-polymers1,33820
Water12,070670
1
C: Kelch-like ECH-associated protein 1
Z: Designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5828
Polymers32,1852
Non-polymers3976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-14 kcal/mol
Surface area11700 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
Y: Designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5668
Polymers32,1692
Non-polymers3976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-21 kcal/mol
Surface area12000 Å2
MethodPISA
3
A: Kelch-like ECH-associated protein 1
X: Designed peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,77310
Polymers32,2292
Non-polymers5448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-19 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.758, 133.933, 82.320
Angle α, β, γ (deg.)90.000, 101.356, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Kelch-like ECH-associated protein ... , 3 types, 3 molecules CBA

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31657.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31641.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#3: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31701.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145

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Protein/peptide , 1 types, 3 molecules XYZ

#4: Protein/peptide Designed peptide


Mass: 527.635 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 690 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H7NS / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride hexahydrate 20% w/v PEG 3350 + 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.698→19.744 Å / Num. obs: 87658 / % possible obs: 95.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 12.88 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.084 / Rrim(I) all: 0.14 / Net I/σ(I): 7.5
Reflection shellResolution: 1.698→1.727 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.079 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4387 / CC1/2: 0.537 / Rpim(I) all: 0.828 / Rrim(I) all: 1.368 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIXdev_5373refinement
XDSVERSION Jun 30, 2024 BUILT=20240723data reduction
AimlessVersion 0.8.1data scaling
PHASERphasing
autoPROC1.0.5 ()data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.74 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.0438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 7022 5.03 %
Rwork0.1605 132444 -
obs0.1626 87658 76.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 141 670 7418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00996923
X-RAY DIFFRACTIONf_angle_d1.069408
X-RAY DIFFRACTIONf_chiral_restr0.0628992
X-RAY DIFFRACTIONf_plane_restr0.01191245
X-RAY DIFFRACTIONf_dihedral_angle_d13.51322484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.29492040.27943375X-RAY DIFFRACTION59.04
1.72-1.740.3421950.27823399X-RAY DIFFRACTION59.74
1.74-1.760.28932100.27913602X-RAY DIFFRACTION62.33
1.76-1.780.33762150.25874017X-RAY DIFFRACTION70.47
1.78-1.80.26342120.24024394X-RAY DIFFRACTION74.74
1.8-1.830.26541880.22734477X-RAY DIFFRACTION76.9
1.83-1.850.25192290.21114402X-RAY DIFFRACTION76.42
1.85-1.880.24272460.21384419X-RAY DIFFRACTION77.03
1.88-1.910.27182130.21414465X-RAY DIFFRACTION76.7
1.91-1.940.25422290.20984420X-RAY DIFFRACTION76.56
1.94-1.980.23212360.17954469X-RAY DIFFRACTION77.91
1.98-2.010.23592440.1714524X-RAY DIFFRACTION77.95
2.01-2.050.22692380.17444424X-RAY DIFFRACTION77.16
2.05-2.090.19182150.16914471X-RAY DIFFRACTION77.53
2.09-2.140.19792290.16564472X-RAY DIFFRACTION77.91
2.14-2.190.20792320.16284519X-RAY DIFFRACTION77.5
2.19-2.240.19992550.15534458X-RAY DIFFRACTION77.58
2.24-2.30.1862360.14944411X-RAY DIFFRACTION76.46
2.3-2.370.24312120.14894283X-RAY DIFFRACTION74.11
2.37-2.450.21272140.15233753X-RAY DIFFRACTION65.61
2.45-2.530.19462490.15324153X-RAY DIFFRACTION72.6
2.53-2.640.19262340.13864798X-RAY DIFFRACTION83
2.64-2.760.18452530.14054871X-RAY DIFFRACTION83.49
2.76-2.90.19092510.1294859X-RAY DIFFRACTION84.07
2.9-3.080.16522710.13184797X-RAY DIFFRACTION84.13
3.08-3.320.1862550.13914880X-RAY DIFFRACTION84.62
3.32-3.650.18222950.14054738X-RAY DIFFRACTION82.85
3.65-4.170.16592820.12944795X-RAY DIFFRACTION83.5
4.17-5.240.15412440.11964915X-RAY DIFFRACTION84.73
5.24-19.740.21732360.19414884X-RAY DIFFRACTION84.16

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