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- PDB-9qbs: KEAP1 complexed to cyclic peptide 33 -

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Basic information

Entry
Database: PDB / ID: 9qbs
TitleKEAP1 complexed to cyclic peptide 33
Components
  • Cyclic peptide
  • Kelch-like ECH-associated protein 1
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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / midbody / Potential therapeutics for SARS / in utero embryonic development / ubiquitin-dependent protein catabolic process / 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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJi, X. / Lau, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Generation of membrane-permeable cyclic peptides inhibiting protein-protein interaction.
Authors: Ji, X. / Farrera-Soler, L. / Li, J. / Sangouard, G. / De Sadeleer, N. / Nielsen, A.L. / Mothukuri, G.K. / Zarda, A. / Will, E.J. / Pojer, F. / Lau, K. / Heinis, C.
History
DepositionMar 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_related_exp_data_set
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
C: Cyclic peptide
D: Cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,57211
Polymers65,0174
Non-polymers5557
Water6,828379
1
A: Kelch-like ECH-associated protein 1
D: Cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9097
Polymers32,5092
Non-polymers4005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
C: Cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6634
Polymers32,5092
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.847, 100.847, 126.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 31625.381 Da / Num. of mol.: 2
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/peptide Cyclic peptide


Mass: 883.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: CSII B6, 0.15 M Potassium thiocyanate, 0.1 M Sodium Acetate, pH 5.5, 20% v/v PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→19.541 Å / Num. obs: 48099 / % possible obs: 99.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.051 / Rrim(I) all: 0.149 / Net I/σ(I): 11.7
Reflection shellResolution: 1.948→1.982 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2155 / CC1/2: 0.674 / Rpim(I) all: 0.368 / Rrim(I) all: 0.945 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX2.0rc1-5599refinement
XDSJun 30, 2024 (BUILT 20241002)data reduction
Aimless0.8.1data scaling
PHASERphasing
autoPROCautoPROC 1.0.5 ()data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.54 Å / SU ML: 0.1897 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2011 2415 5.02 %
Rwork0.168 45648 -
obs0.1697 48063 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 128 379 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694651
X-RAY DIFFRACTIONf_angle_d0.8746319
X-RAY DIFFRACTIONf_chiral_restr0.062662
X-RAY DIFFRACTIONf_plane_restr0.0079840
X-RAY DIFFRACTIONf_dihedral_angle_d16.63131701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.25971180.22722437X-RAY DIFFRACTION91.48
1.99-2.030.27221410.20692662X-RAY DIFFRACTION100
2.03-2.080.24641600.19252625X-RAY DIFFRACTION100
2.08-2.130.25931330.19022671X-RAY DIFFRACTION99.96
2.13-2.190.2241250.18312690X-RAY DIFFRACTION100
2.19-2.250.24931550.17992626X-RAY DIFFRACTION99.96
2.25-2.320.23881260.17922672X-RAY DIFFRACTION100
2.32-2.410.25341390.18262683X-RAY DIFFRACTION100
2.41-2.50.22181260.18332692X-RAY DIFFRACTION99.96
2.5-2.620.19921590.18162669X-RAY DIFFRACTION100
2.62-2.760.20941650.17692670X-RAY DIFFRACTION99.93
2.76-2.930.19191340.16912684X-RAY DIFFRACTION99.96
2.93-3.150.22661430.1822728X-RAY DIFFRACTION100
3.15-3.470.19911350.15752728X-RAY DIFFRACTION100
3.47-3.970.17731480.14992732X-RAY DIFFRACTION99.97
3.97-4.980.13861600.12122762X-RAY DIFFRACTION100
4.98-19.540.18651480.17492917X-RAY DIFFRACTION99.77

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