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- PDB-4iqk: Crystal structure of cpd 16 bound to Keap1 Kelch domain -

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Basic information

Entry
Database: PDB / ID: 4iqk
TitleCrystal structure of cpd 16 bound to Keap1 Kelch domain
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION
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-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 / 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-IQK / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSilvian, L. / Marcotte, D.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Small molecules inhibit the interaction of Nrf2 and the Keap1 Kelch domain through a non-covalent mechanism.
Authors: Marcotte, D. / Zeng, W. / Hus, J.C. / McKenzie, A. / Hession, C. / Jin, P. / Bergeron, C. / Lugovskoy, A. / Enyedy, I. / Cuervo, H. / Wang, D. / Atmanene, C. / Roecklin, D. / Vecchi, M. / ...Authors: Marcotte, D. / Zeng, W. / Hus, J.C. / McKenzie, A. / Hession, C. / Jin, P. / Bergeron, C. / Lugovskoy, A. / Enyedy, I. / Cuervo, H. / Wang, D. / Atmanene, C. / Roecklin, D. / Vecchi, M. / Vivat, V. / Kraemer, J. / Winkler, D. / Hong, V. / Chao, J. / Lukashev, M. / Silvian, L.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0602
Polymers32,5621
Non-polymers4991
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.856, 75.638, 48.341
Angle α, β, γ (deg.)90.000, 106.090, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a monomer

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Components

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


Mass: 32561.510 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN RESIDUES 321-609 / Mutation: E540A, E542A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INRF2, KEAP1, KIAA0132, KLHL19 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus(DE3)-RIL / References: UniProt: Q14145
#2: Chemical ChemComp-IQK / N,N'-naphthalene-1,4-diylbis(4-methoxybenzenesulfonamide)


Mass: 498.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N2O6S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 3.5M Na Formate, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2010 / Details: MONOCHROMATOR
RadiationMonochromator: Kohzu HLD-4 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→19.913 Å / Num. obs: 30805 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.97-2.083.80.8410.71677744720.841100
2.08-2.23.80.5511.11613542890.551100
2.2-2.353.80.3831.51497739750.383100
2.35-2.543.80.2762.41411637390.276100
2.54-2.793.80.1741289133990.17100
2.79-3.113.80.1185.61178531070.118100
3.11-3.63.80.1065.91041227480.106100
3.6-4.413.80.0797.3883423350.079100
4.41-6.233.70.068.7667017960.0699.9
6.23-19.9133.50.0688.832689450.06892.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→19.42 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.653 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 1549 5 %RANDOM
Rwork0.1533 ---
obs0.1546 30772 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.97 Å2 / Biso mean: 28.3695 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.97→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 34 122 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192275
X-RAY DIFFRACTIONr_bond_other_d0.0010.022056
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9513102
X-RAY DIFFRACTIONr_angle_other_deg0.96234687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10622.453106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7751522
X-RAY DIFFRACTIONr_chiral_restr0.1130.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212658
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02582
X-RAY DIFFRACTIONr_mcbond_it2.0432.4241139
X-RAY DIFFRACTIONr_mcbond_other2.0442.4231138
X-RAY DIFFRACTIONr_mcangle_it2.9643.6261422
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.15 102 -
Rwork0.096 2131 -
all-2233 -
obs--99.24 %

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