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- PDB-7xm2: Crystal structure of Keap1 Kelch domain (residues 322-609) in com... -

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Basic information

Entry
Database: PDB / ID: 7xm2
TitleCrystal structure of Keap1 Kelch domain (residues 322-609) in complex with NXPZ-2
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / oxidative stress sensor
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
Chem-GFD / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, K.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Crystallography-Guided Optimizations of the Keap1-Nrf2 Inhibitors on the Solvent Exposed Region: From Symmetric to Asymmetric Naphthalenesulfonamides.
Authors: Liu, G. / Hou, R. / Xu, L. / Zhang, X. / Yan, J. / Xing, C. / Xu, K. / Zhuang, C.
History
DepositionApr 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers31,9371
Non-polymers1,1952
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11520 Å2
Unit cell
Length a, b, c (Å)126.256, 75.619, 48.651
Angle α, β, γ (deg.)90.000, 106.386, 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

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


Mass: 31936.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-GFD / 2-[(4-aminophenyl)sulfonyl-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]amino]ethanamide


Mass: 597.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19560 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.68 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.67 / Num. unique obs: 1932

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XMB

4xmb


Resolution: 2.3→46.67 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.7729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 3814 10.01 %
Rwork0.1677 34281 -
obs0.1725 19556 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 41 127 2370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632310
X-RAY DIFFRACTIONf_angle_d0.98763157
X-RAY DIFFRACTIONf_chiral_restr0.0555324
X-RAY DIFFRACTIONf_plane_restr0.0049413
X-RAY DIFFRACTIONf_dihedral_angle_d16.8472338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.30961370.24071223X-RAY DIFFRACTION97.35
2.33-2.360.26631370.22381251X-RAY DIFFRACTION99.36
2.36-2.390.21441390.21131231X-RAY DIFFRACTION99.49
2.39-2.420.24111470.21981345X-RAY DIFFRACTION99.47
2.42-2.460.25841390.21581228X-RAY DIFFRACTION99.42
2.46-2.50.29311400.21291291X-RAY DIFFRACTION99.44
2.5-2.540.28841420.21171302X-RAY DIFFRACTION99.52
2.54-2.580.25161420.21231252X-RAY DIFFRACTION99.5
2.58-2.630.28071400.21421274X-RAY DIFFRACTION99.58
2.63-2.680.31681430.19091279X-RAY DIFFRACTION99.51
2.68-2.740.2721420.20041278X-RAY DIFFRACTION99.44
2.74-2.80.25621390.17611251X-RAY DIFFRACTION98.3
2.8-2.860.20221400.16311269X-RAY DIFFRACTION99.02
2.86-2.930.23611430.17131276X-RAY DIFFRACTION99.79
2.93-3.010.22381390.16931281X-RAY DIFFRACTION99.58
3.01-3.10.23731430.17791258X-RAY DIFFRACTION99.5
3.1-3.20.22151380.15981291X-RAY DIFFRACTION99.72
3.2-3.310.1881450.16411276X-RAY DIFFRACTION99.86
3.32-3.450.20791450.14091274X-RAY DIFFRACTION99.58
3.45-3.60.17851440.16051282X-RAY DIFFRACTION99.58
3.6-3.790.21831390.14941244X-RAY DIFFRACTION98.15
3.79-4.030.20971460.15051288X-RAY DIFFRACTION99.65
4.03-4.340.16881430.12281267X-RAY DIFFRACTION99.23
4.34-4.780.14681410.12261262X-RAY DIFFRACTION99.22
4.78-5.470.16041420.15121285X-RAY DIFFRACTION99.03
5.47-6.890.24541420.18381277X-RAY DIFFRACTION99.65
6.89-46.670.23961370.19721246X-RAY DIFFRACTION97.39

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