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- PDB-8pkw: Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene lin... -

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Basic information

Entry
Database: PDB / ID: 8pkw
TitleKelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 5 (ortho-WRCDPETaEC).
Components
  • CP5
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / Peptide inhibitor / Inhibitor complex / cyclic peptide / Ubiquitin ligase / NRF2
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / 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-methylphenyl)methanol / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsBraun, M.B. / Bischof, L. / Hartmann, M.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2023
Title: Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders.
Authors: Fonseca Lopez, F. / Miao, J. / Damjanovic, J. / Bischof, L. / Braun, M.B. / Ling, Y. / Hartmann, M.D. / Lin, Y.S. / Kritzer, J.A.
History
DepositionJun 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 13, 2023Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
P: CP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,30715
Polymers70,4843
Non-polymers82312
Water6,648369
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1159
Polymers34,6251
Non-polymers4908
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
P: CP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1926
Polymers35,8592
Non-polymers3334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.684, 68.970, 77.965
Angle α, β, γ (deg.)90.000, 117.864, 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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Protein / Protein/peptide , 2 types, 3 molecules ABP

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


Mass: 34624.793 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 CP5


Mass: 1234.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 381 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-ZK2 / (2-methylphenyl)methanol


Mass: 122.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris pH 6.5, 1.5 M NH4SO4, 0.2 % PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.54→42.13 Å / Num. obs: 112741 / % possible obs: 99.8 % / Redundancy: 6.77 % / Biso Wilson estimate: 30.61 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.86
Reflection shellResolution: 1.54→1.63 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 18156 / CC1/2: 0.567 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→42.13 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2255 2 %
Rwork0.1575 110461 -
obs0.1583 112716 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.86 Å2
Refinement stepCycle: LAST / Resolution: 1.54→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 47 369 4794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514707
X-RAY DIFFRACTIONf_angle_d0.77156455
X-RAY DIFFRACTIONf_chiral_restr0.0563692
X-RAY DIFFRACTIONf_plane_restr0.0042865
X-RAY DIFFRACTIONf_dihedral_angle_d4.37633570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.32171400.29966888X-RAY DIFFRACTION99.96
1.57-1.610.36931400.27126865X-RAY DIFFRACTION99.96
1.61-1.650.30911410.26376885X-RAY DIFFRACTION99.93
1.65-1.70.34291400.28196878X-RAY DIFFRACTION99.99
1.7-1.740.29381400.24256835X-RAY DIFFRACTION99.94
1.74-1.80.24941410.1966885X-RAY DIFFRACTION99.96
1.8-1.870.20761400.15946885X-RAY DIFFRACTION99.99
1.87-1.940.20731410.14696901X-RAY DIFFRACTION100
1.94-2.030.17561400.14476885X-RAY DIFFRACTION100
2.03-2.140.2091410.15166869X-RAY DIFFRACTION100
2.14-2.270.19411410.15776927X-RAY DIFFRACTION99.97
2.27-2.440.21641410.15386900X-RAY DIFFRACTION100
2.44-2.690.2171410.16626918X-RAY DIFFRACTION99.99
2.69-3.080.17161410.1566921X-RAY DIFFRACTION99.92
3.08-3.880.18931420.14686968X-RAY DIFFRACTION99.93
3.88-42.130.18251450.14357051X-RAY DIFFRACTION99.81

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