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

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Basic information

Entry
Database: PDB / ID: 8pkv
TitleKelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 4 (ortho-WRCDPETGEC).
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 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / 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 / ubiquitin-dependent protein catabolic process / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 motif / Kelch / 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 motif / Kelch / 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: 1.55 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Dec 25, 2024Group: Structure summary / Category: struct / Item: _struct.title

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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: CP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,07330
Polymers70,4703
Non-polymers1,60427
Water6,900383
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,49818
Polymers34,6251
Non-polymers87317
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)36,57612
Polymers35,8452
Non-polymers73110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.957, 68.861, 77.950
Angle α, β, γ (deg.)90.000, 117.655, 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
Components on special symmetry positions
IDModelComponents
11B-703-

NA

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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: 1220.336 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, 410 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / 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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 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: 1.55→42.19 Å / Num. obs: 107030 / % possible obs: 96.4 % / Redundancy: 7.07 % / Biso Wilson estimate: 30.97 Å2 / CC1/2: 1 / Net I/σ(I): 18.77
Reflection shellResolution: 1.55→1.64 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 16859 / CC1/2: 0.495

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.19 Å / SU ML: 0.2641 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 2141 2 %
Rwork0.1571 104864 -
obs0.1578 107005 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.29 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 90 383 4875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054849
X-RAY DIFFRACTIONf_angle_d0.78156648
X-RAY DIFFRACTIONf_chiral_restr0.0565708
X-RAY DIFFRACTIONf_plane_restr0.0043891
X-RAY DIFFRACTIONf_dihedral_angle_d17.6861702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.46891380.48076761X-RAY DIFFRACTION94.36
1.59-1.630.4181400.39746856X-RAY DIFFRACTION94.72
1.63-1.670.29871400.29356831X-RAY DIFFRACTION95.14
1.67-1.720.30421400.23456897X-RAY DIFFRACTION95.43
1.72-1.770.22631400.19556862X-RAY DIFFRACTION95.56
1.77-1.840.21161410.17126906X-RAY DIFFRACTION96.01
1.84-1.910.20831420.1666949X-RAY DIFFRACTION96.25
1.91-20.1991430.16546983X-RAY DIFFRACTION96.56
2-2.10.17091420.14456994X-RAY DIFFRACTION96.77
2.1-2.240.19281440.14357027X-RAY DIFFRACTION97.14
2.24-2.410.17371430.14497037X-RAY DIFFRACTION97.54
2.41-2.650.1871460.1647110X-RAY DIFFRACTION97.88
2.65-3.030.20351450.15737121X-RAY DIFFRACTION98.26
3.03-3.820.17921470.14597194X-RAY DIFFRACTION98.59
3.82-42.190.17531500.14077336X-RAY DIFFRACTION98.85

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