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- PDB-8pku: Kelch domain of KEAP1 in complex with ortho-dimethylbenzene linke... -

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Basic information

Entry
Database: PDB / ID: 8pku
TitleKelch domain of KEAP1 in complex with ortho-dimethylbenzene linked cyclic peptide 3 (ortho-WRCDEETGEC).
Components
  • CP3
  • 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 / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / regulation of autophagy / Ub-specific processing proteases / protein ubiquitination / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
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-methylphenyl)methanol / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBraun, M.B. / Bischof, L. / Hartmann, M.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: 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 2.0Dec 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct / struct_conn / struct_ref_seq
Item: _atom_site.label_seq_id / _chem_comp.formula ..._atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct.title / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Oct 23, 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: CP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09723
Polymers70,5023
Non-polymers1,59520
Water4,666259
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,53913
Polymers34,6251
Non-polymers91412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
P: CP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,55810
Polymers35,8772
Non-polymers6818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.960, 68.583, 77.720
Angle α, β, γ (deg.)90.000, 117.450, 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 CP3


Mass: 1252.335 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)

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Non-polymers , 6 types, 279 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.: 1 / Source method: obtained synthetically / Formula: Cl
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6O2
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 0.99988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.73→42.1 Å / Num. obs: 78891 / % possible obs: 99.7 % / Redundancy: 6.72 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.08
Reflection shellResolution: 1.73→1.83 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 12656 / CC1/2: 0.592 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→42.1 Å / SU ML: 0.2109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2058 2129 2.7 %
Rwork0.181 76713 -
obs0.1817 78842 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.78 Å2
Refinement stepCycle: LAST / Resolution: 1.73→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 96 259 4745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614789
X-RAY DIFFRACTIONf_angle_d0.82786550
X-RAY DIFFRACTIONf_chiral_restr0.0603697
X-RAY DIFFRACTIONf_plane_restr0.0053870
X-RAY DIFFRACTIONf_dihedral_angle_d6.22053619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.36961420.37325077X-RAY DIFFRACTION99.73
1.77-1.810.29341400.31755069X-RAY DIFFRACTION99.64
1.81-1.860.31631410.27255074X-RAY DIFFRACTION99.85
1.86-1.920.30021420.26435099X-RAY DIFFRACTION99.85
1.92-1.980.25171420.2235100X-RAY DIFFRACTION99.89
1.98-2.050.22651400.20225070X-RAY DIFFRACTION99.87
2.05-2.130.20661420.18845116X-RAY DIFFRACTION99.94
2.13-2.230.19571420.18875116X-RAY DIFFRACTION100
2.23-2.350.20791410.18565113X-RAY DIFFRACTION99.89
2.35-2.490.18851410.19545091X-RAY DIFFRACTION99.87
2.49-2.690.22011420.1995108X-RAY DIFFRACTION99.96
2.69-2.960.20981420.18445126X-RAY DIFFRACTION99.92
2.96-3.390.23661430.18245155X-RAY DIFFRACTION99.89
3.39-4.270.18841430.15145141X-RAY DIFFRACTION99.89
4.27-42.10.17491460.16355258X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.320089032575.05660502872-3.88919935646.6517674388-5.222226278415.886685190530.01988917399780.346118536456-0.210667062591-0.2947758868530.0276939351870.1622384814370.136904086787-0.03676587128580.1896027157620.3484493457410.0129125932804-0.02162238708980.291015731419-0.04750341508730.366437215613-37.04915.322-3.435
22.796781843952.410305829430.0898990027525.89177327330.07491606837030.865205598564-0.1048694325470.2065435889840.0121807150828-0.3857772582980.03356918544540.110388938390.0125852286905-0.0439373201220.08640355042710.2831409745680.0270041007991-0.02140749692210.2640218002010.00625445703970.305292604055-39.52220.087-0.41
35.060595089940.6437504600090.5374026895912.36972671232-0.1275899015792.54851733826-0.0978725464909-0.16155346330.2518692939380.125199269175-0.01839460861410.0415950154082-0.1950667062530.044879873390.1349761435320.311051011810.0250357268115-0.008258545860560.2015421842970.00229704413940.297045287268-35.12627.6467.294
43.44194321147-1.362282425510.715386464432.29024812918-0.5242859328481.42228279421-0.164179973073-0.505669916790.0917238796070.5254577398520.0832488328227-0.0310810375325-0.1292332423410.008725447667960.07787935431750.384536266862-0.00907627228044-0.02184856336780.3547459499570.008849770370060.285693620967-27.12323.60117.06
52.10370103510.2116943926290.0773254491211.97959389149-0.1756232395652.372679435340.0396456336714-0.16450245738-0.3075409939550.14703835158-0.06123626084920.02664903887540.2199156228930.05371466098510.02559902123390.302188547082-0.00763469886370.012029013830.2533811355930.02302076391030.328118012274-29.6377.0998.096
61.854491891630.7210011891850.7978354824681.51345511115-1.533559144923.120253262790.4198547909212.33778671812.23935663570.1188375926350.2856234607771.1352696673-0.978100354348-2.07187561843-0.173886248180.4112290413530.388587397859-0.07101762013691.783801848970.9111203339760.916954602617-53.86426.03545.952
71.35960581191.18431659645-0.04576188366161.37287442213-0.8325790687892.20641098311-0.5686850298412.2366857959-0.0386186626717-0.443177265860.3957139500190.2943192968250.529262829277-1.892545585860.001680926008320.426768969916-0.240723171362-0.02956748239341.4668618261-0.04190933071260.423925835235-52.12413.19149.758
83.21927292388-0.479317102231-0.8312484586831.67541544885-0.8069619252920.653106864982-1.516954033691.68875256917-2.1986486796-0.4073673107370.4332427415890.1874768434821.86010416807-1.058147622550.1058293050890.737736377009-0.4887362121180.2868037602410.976242505109-0.4033423478220.821074555047-41.0585.9347.844
96.706194607781.68037837787-3.925564179152.69777238586-0.6169338913076.03462476949-0.8271162662610.756641326373-1.05257186539-0.3766079016990.129924657065-0.3958558419960.685123987893-0.2328630502920.5221798086860.35156995894-0.07015804727990.1129056033440.475546108259-0.03670294728590.404764674511-29.52913.13147.108
103.901184276221.27474130873-1.235958249122.03847417608-1.619016109932.824109598550.5157595176671.487958593161.70500238479-0.07723802042940.5788016325580.522635381982-0.953770240107-1.03921260909-0.3352350468240.6130829160390.1284753242330.09932154734660.9006973292160.5302920321080.788720912813-37.28929.61145.004
110.747525868041-0.676600083498-0.108100788512.691770479230.1941053520070.975495256272-0.307315625782.12929259801-0.158544001876-0.3271892972990.546961372790.8642122302860.0519127185233-0.9561215566790.08971938869480.0585678842518-0.00483286935877-0.3846281965962.444478104020.5076779178480.592700334264-52.39821.07939.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 325:341 )A325 - 341
2X-RAY DIFFRACTION2( CHAIN A AND RESID 342:395 )A342 - 395
3X-RAY DIFFRACTION3( CHAIN A AND RESID 396:442 )A396 - 442
4X-RAY DIFFRACTION4( CHAIN A AND RESID 443:517 )A443 - 517
5X-RAY DIFFRACTION5( CHAIN A AND RESID 518:613 )A518 - 613
6X-RAY DIFFRACTION6( CHAIN B AND RESID 326:353 )B326 - 353
7X-RAY DIFFRACTION7( CHAIN B AND RESID 354:416 )B354 - 416
8X-RAY DIFFRACTION8( CHAIN B AND RESID 417:451 )B417 - 451
9X-RAY DIFFRACTION9( CHAIN B AND RESID 452:506 )B452 - 506
10X-RAY DIFFRACTION10( CHAIN B AND RESID 507:602 )B507 - 602
11X-RAY DIFFRACTION11( CHAIN B AND RESID 603:613 )B603 - 613

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