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- PDB-5daf: Crystal Structure of Human KEAP1 BTB Domain in Complex with Small... -

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Basic information

Entry
Database: PDB / ID: 5daf
TitleCrystal Structure of Human KEAP1 BTB Domain in Complex with Small Molecule TX64063
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / KEAP1 / Trascription Regulation / BTB domain / Cysteine Modification / C1-(R)-Cys151 adduct
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 / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-58E / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsHuerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. ...Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Swinger, K.K. / Stoll, V.S. / Ferguson, D.A. / Thomas, P.J. / Probst, B. / Dulubova, I. / Visnick, M. / Wigley, W.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Characterization of novel small-molecule NRF2 activators: Structural and biochemical validation of stereospecific KEAP1 binding.
Authors: Huerta, C. / Jiang, X. / Trevino, I. / Bender, C.F. / Ferguson, D.A. / Probst, B. / Swinger, K.K. / Stoll, V.S. / Thomas, P.J. / Dulubova, I. / Visnick, M. / Wigley, W.C.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification

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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)15,9292
Polymers15,5951
Non-polymers3341
Water39622
1
A: Kelch-like ECH-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)31,8594
Polymers31,1902
Non-polymers6692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area3920 Å2
ΔGint-35 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.449, 42.449, 134.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

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


Mass: 15594.950 Da / Num. of mol.: 1 / Fragment: UNP residues 49-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q14145
#2: Chemical ChemComp-58E / (5aS,6S,9aS)-7-hydroxy-2,6,9a-trimethyl-3-(pyridin-3-yl)-4,5,5a,6,9,9a-hexahydro-2H-benzo[g]indazole-8-carbonitrile


Mass: 334.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES, pH 9.5, 30% w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2012 / Details: Pixel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.369→134.044 Å / Num. obs: 5900 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 31.6 / Num. measured all: 55344
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all
2.369-2.3779.90.349649550
10.994-134.0446.90.03251475

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XDSautoPROC, XDS (VERSION December 6, 2010)data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→44.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2487 / WRfactor Rwork: 0.2119 / FOM work R set: 0.7701 / SU B: 9.558 / SU ML: 0.204 / SU R Cruickshank DPI: 0.3782 / SU Rfree: 0.2359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 266 4.5 %RANDOM
Rwork0.2021 ---
obs0.2035 5591 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.8 Å2 / Biso mean: 63.126 Å2 / Biso min: 35.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 2.37→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 25 22 989
Biso mean--79.75 65.73 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02987
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9851338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71924.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61815172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.613153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02724
LS refinement shellResolution: 2.369→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 21 -
Rwork0.331 366 -
all-387 -
obs--100 %

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