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

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Basic information

Entry
Database: PDB / ID: 8pkx
TitleKelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 11 (ortho-WRCNPETaEC).
Components
  • CP11
  • 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 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / 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 / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / 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 / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / 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 motif / Kelch repeat type 1 / 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 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-methylphenyl)methanol / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
P: CP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,60521
Polymers70,4833
Non-polymers1,12218
Water5,206289
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,19712
Polymers34,6251
Non-polymers57211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
P: CP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4089
Polymers35,8582
Non-polymers5507
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.430, 68.877, 78.252
Angle α, β, γ (deg.)90.000, 117.676, 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 CP11


Mass: 1233.377 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, 307 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.77 Å3/Da / Density % sol: 60 %
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: 0.99999 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: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.79→42.24 Å / Num. obs: 72288 / % possible obs: 99.6 % / Redundancy: 6.93 % / Biso Wilson estimate: 35.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.53
Reflection shellResolution: 1.79→1.9 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 11545 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→42.24 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 2313 3.2 %
Rwork0.1749 69956 -
obs0.176 72269 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.66 Å2
Refinement stepCycle: LAST / Resolution: 1.79→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 67 289 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614745
X-RAY DIFFRACTIONf_angle_d0.83566508
X-RAY DIFFRACTIONf_chiral_restr0.0616702
X-RAY DIFFRACTIONf_plane_restr0.0046868
X-RAY DIFFRACTIONf_dihedral_angle_d17.84331668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.820.32861340.31634041X-RAY DIFFRACTION97.8
1.82-1.860.31851360.29834107X-RAY DIFFRACTION99.91
1.86-1.910.3491350.30314077X-RAY DIFFRACTION99.86
1.91-1.960.29641340.26044069X-RAY DIFFRACTION99.98
1.96-2.010.26661360.22494118X-RAY DIFFRACTION99.95
2.01-2.070.24671360.20654099X-RAY DIFFRACTION100
2.07-2.130.26111350.1944095X-RAY DIFFRACTION99.98
2.13-2.210.19151360.18494110X-RAY DIFFRACTION99.98
2.21-2.30.2331360.1824108X-RAY DIFFRACTION99.98
2.3-2.40.22041350.18164102X-RAY DIFFRACTION99.93
2.4-2.530.22441360.1924122X-RAY DIFFRACTION100
2.53-2.690.23451360.194118X-RAY DIFFRACTION99.95
2.69-2.90.22051370.17634145X-RAY DIFFRACTION99.98
2.9-3.190.19341360.17674104X-RAY DIFFRACTION100
3.19-3.650.16541370.16434135X-RAY DIFFRACTION99.91
3.65-4.60.18651370.1314170X-RAY DIFFRACTION99.88
4.6-42.240.20691410.16964236X-RAY DIFFRACTION99.73

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